I have been fighting this issue and it's officially driving me crazy.
We have 2 mac pros running Server 5.3.1. I see other users that have the problem of updates disabling themselves, well I have the opposite problem. Updates that I have marked as Disabled or remove are automatically downloading and enabled. I have "Automatically download new updates" unchecked. I watched as after first disabling the updates I don't need, then monitoring the storage and seeing the storage slowly decreasing as updates are being re-downloaded.
I have even deleted the the server app and the updates, only to have the issue pop again after setting cup the server again. Any suggestions would be greatly appreciated
This has been a long standing bug (feature?) with Mac server, the worst part for us is its the only module of the cluster that is server we utilize. You can see this thread https://discussions.apple.com/thread/6833868?start=0&tstart=0 you need to delete the updates in server then quickly run this terminal command. Also be careful Its requires 15% free hard drive space of the size of the partition its on. I ran into an issue where updates were not downloading, opened a case with apple turned out we had a "full:hard drive. Actually I only had 100 gigs free but by % it was not enough and the updates stop downloading. Great engineering on that one. The best part the only error that stats that shows up in the logs if you turn on debug level so you don't actually know its an issue.
Now that you mentioned this I agree with you and watching my own instance I agree with you. This is very annoying. I am actually fighting with this stupid thing to have it download the latest version of ITunes.
I have been working on this issue fro a few days now. I may have the issue licked. Not completeley sure, however nothing has been downloaded in the last 15 minutes and no network traffic. I used Bbedit to open /Library/Server/Software Update/Status/com.apple.server.swupdate.plist
After which I used the find and replace the "enable" key to "disable" to the end
I had the plist open and noticed disable and changed back to enable