I didn't have any luck on the apple forums.

Join the club! :-)

Hopefully someone chimes in with an easier solution than mine.

For many years Software Update Server would frequently break on me on different servers at many different locations. When it would break I quit banging my head against the wall with trying to fix it and would just reset it back to default. 3-4 years ago it stopped breaking on me so I haven't had to reset to defaults in a long time. Now I don't remember how to reset it.

I tried to search for the procedure just now and was finding old info that may be outdated.

Dang seems like when they removed server admin, OS X server when to hell thanks for the reply though ill update this if i get anywhere.

Ha I just found this by modifying my keyword search a bit.
https://support.apple.com/en-us/HT200272

Isn't quite in keeping with my senario but ill give it a go this server isn't in production yet. thanks

@Matt.Ellis i wonder if it's an issue with the available space?

I've detailed what I saw when that was my issue here

Ill 2nd the available space piece,
I found that it suddenly stops download updates and then appears to not do anything else. But if you check the server logs for softwareupdateserver you will see messages for disk full (it usually saves a certain percentage of the drive for free space).

Gabe Shackney
Princeton Public Schools

In my case it shouldn't be a space issue. I have about 600gb available on the server. Ill double check when i get back into town just finished up my cca today :)

So i did verify it, i have 600gb of space still open, i can try upgrading to the newest Server App, and see if that helps? im also going to search thought the log today as @gshackney recommended

Also I've found that setting the server to store the data on a separate drive, aside from the boot drive, had issues. I eventually got this working, and I think the newest Server app helped this a bit.

Gabe Shackney
Princeton Public Schools

So everything is stored on one drive, i upgraded to 10.11.1 and updated the server app to 5.0.15, Enabled the updates i wanted. Was able to update my computer with them. a few hours later all show as disabled in server app.

Since this server isn't in production yet im half tempted to wipe the whole thing and start again maybe something got corrupted in an update.

I am seeing this as well - OS X 10.10.5 with Server 5.0.4 - updates saving to the standard place on the system volume. I have set the system volume reserve to 10%, and the permissions on the config files are good. I go in and enable updates (10.11 updates in this case) and a couple of hours later they are disabled again.

Glad its not just me, i am going to put in a call with Apple enterprise support later today. if i get any info from them i will post it here.

So they have no initial clue, there asking me to run a log capture after the updates disable themselves so hopefully i can get that to then in a few hours.

Hi from France. FYI, I confirm that the issue is still there with Server 5.0.15 on OS X 10.11.1. The enabled updates are disabled after some minutes or hours. That is really annoying. Did someone yet open an bug report at Apple and have received a "duplicate" status ?

I havent put in a bug report yet as im working with there Enterprise support/ engineering team

We are seeing the same thing. I've opened up case 976946712.

I've wiped and reinstalled with the same behavior after letting it sync up overnight. For us it is every update since 10/1/2015 that goes to the disabled state.

Mac Mini Late 2012
OS 10.11.1
Server 5.0.15

I did a permissions repair on one of my Mini DPs first thing this morning, and so far the enablement status of 10.11 updates is holding steady. Stay tuned.

Ill give that a shot, still havent heard back from apple. So i can't run disk permissions as im on 10.11 and it does that automajically but System integrity protection is on and should be maintaining that.

Scratch that the updates just disabled themselves again. Here is what I am seeing in the swupd log file for the sync:

Nov 2 09:45:34 bosjssdp1.sapient.com swupd_syncd[25388] <Info>: ========== Sync Started ==========
Nov 2 09:45:34 bosjssdp1.sapient.com swupd_syncd[25388] <Info>: Checking service data location: /Library/Server/Software Update/Data/html
Nov 2 09:45:34 bosjssdp1.sapient.com swupd_syncd[25388] <Info>: Retrieving catalog list
Nov 2 09:45:34 bosjssdp1.sapient.com swupd_syncd[25388] <Info>: Retrieving deprecated updates list
2015-11-02 09:45:34.738 swupd_syncd[25388:1711160] Failed to obtain sandbox extension for path=/var/empty/Library/Caches/swupd_syncd. Errno:2
Nov 2 09:45:35 bosjssdp1.sapient.com swupd_syncd[25388] <Info>: Retrieving remote catalog (STANDARD): index-10.11-10.10-10.9-mountainlion-lion-snowleopard-leopard.merged-1.sucatalog
Nov 2 09:45:37 bosjssdp1.sapient.com swupd_syncd[25388] <Info>: Retrieving remote catalog (STANDARD): index-10.10-10.9-mountainlion-lion-snowleopard-leopard.merged-1.sucatalog
Nov 2 09:45:40 bosjssdp1.sapient.com swupd_syncd[25388] <Info>: Retrieving remote catalog (STANDARD): index-10.9-mountainlion-lion-snowleopard-leopard.merged-1.sucatalog
Nov 2 09:45:41 bosjssdp1.sapient.com swupd_syncd[25388] <Info>: Retrieving remote catalog (STANDARD): index-mountainlion-lion-snowleopard-leopard.merged-1.sucatalog
Nov 2 09:45:42 bosjssdp1.sapient.com swupd_syncd[25388] <Info>: Retrieving remote catalog (STANDARD): index-lion-snowleopard-leopard.merged-1.sucatalog
Nov 2 09:45:44 bosjssdp1.sapient.com swupd_syncd[25388] <Info>: Retrieving remote catalog (STANDARD): index-leopard-snowleopard.merged-1.sucatalog
Nov 2 09:45:46 bosjssdp1.sapient.com swupd_syncd[25388] <Info>: Updating local catalog: index-10.11-10.10-10.9-mountainlion-lion-snowleopard-leopard.merged-1.sucatalog
Nov 2 09:47:38 bosjssdp1.sapient.com swupd_syncd[25388] <Info>: *

Nothing out of the usual...

If you want to open a ticket with apple my case# is 974711947. Claven i gave my rep your case number so they could compare. as it looks like we are on identical software / hardware.

I upgraded one of my DPs to 10.11.1 and am going to watch and see if this problem still pops up...

Installing 10.11.1 did not fix this issue. Updates still disabled... SIGH

Something interesting that I found in the swupdate settings (by running /Applications/Server.app/Contents/ServerRoot/usr/sbin/serveradmin fullstatus swupdate):

swupdate:state = "RUNNING"
swupdate:lastChecktime = 2015-11-02 21:30:05 +0000
swupdate:autoMirrorOnlyNew = no
swupdate:syncServiceState = "RUNNING"
swupdate:startTime = 2015-11-03 15:38:26 +0000
swupdate:lastProductsUpdate = 2015-11-03 15:37:56 +0000
swupdate:logPaths:swupdateServiceLog = "/Library/Server/Software Update/Log/swupd_syncd.log"
swupdate:logPaths:swupdateErrorLog = "/Library/Server/Software Update/Log/swupd_error.log"
swupdate:logPaths:swupdateAccessLog = "/Library/Server/Software Update/Log/swupd_access.log"
swupdate:pluginVers = "10.11.111 (111)"
swupdate:checkError = no
swupdate:autoEnable = no
swupdate:updatesDocRoot = "/Library/Server/Software Update/Data/"
swupdate:hostServiceState = "RUNNING"
swupdate:autoMirror = yes
swupdate:numOfEnabledPkg = 1011
swupdate:servicePortsAreRestricted = "NO"
swupdate:numOfMirroredPkg = 1207
swupdate:setStateVersion = 1
swupdate:syncStatus = "DONE"
swupdate:readWriteSettingsVersion = 1

I have enabled all but two updates in the GUI, so the enabled count should be 1205, not 1011. That is very strange! I submitted a bug report with Apple...

Mines even more fun after enabling about 30 updates i see this: it has to be some sort of bug not showing the correct amount of whats enabled then a process runs about 3 hours later and fixes the UI issue that shows them as enabled.

swupdate
swupdate:state = "RUNNING"
swupdate:lastChecktime = 2015-11-03 11:00:05 +0000
swupdate:autoMirrorOnlyNew = no
swupdate:syncServiceState = "RUNNING"
swupdate:startTime = 2015-10-29 20:41:02 +0000
swupdate:lastProductsUpdate = 2015-11-03 11:14:13 +0000
swupdate:logPaths:swupdateServiceLog = "/Library/Server/Software Update/Log/swupd_syncd.log"
swupdate:logPaths:swupdateErrorLog = "/Library/Server/Software Update/Log/swupd_error.log"
swupdate:logPaths:swupdateAccessLog = "/Library/Server/Software Update/Log/swupd_access.log"
swupdate:pluginVers = "10.11.111 (111)"
swupdate:checkError = no
swupdate:autoEnable = no
swupdate:updatesDocRoot = "/Library/Server/Software Update/Data/"
swupdate:hostServiceState = "RUNNING"
swupdate:autoMirror = yes
swupdate:numOfEnabledPkg = 0
swupdate:servicePortsAreRestricted = "NO"
swupdate:numOfMirroredPkg = 1205
swupdate:setStateVersion = 1
swupdate:syncStatus = "DONE"
swupdate:readWriteSettingsVersion = 1

Hummm appears Server 5.0.15 is out as an update for 5.0.4...