Yosemite 10.10.5, Safari 8.0.8 - Some Configuration Profile Settings not Sticking

[MTFIDjamf]

All -
Still pretty new to all of this and looking at a Config Profile to control Safari settings and plugins. I have built out a machine in our corporate environment with 10.10.5, launched Safari for the first time, set it up a bit and allowed always a bunch of plugins. I then took the plist file, converted to xml and uploaded into the JSS, applied to a few test machines, confirmed the profile is applied to the machines. It seems to be working, however I am getting some odd results randomly.

Settings:
Set our corporate homepage, no issues.
Set Safari opens with, new window pens with, new tabs open with, no issues
Set plugin prefs for Citrix Receiver, Java, Sharepoint Plugin, no issues
Set popups to not be blocked, no issues.

Set Favorites bar to be visible, delete default Safari favs, set 4 corporate links here. This seems to stick for a bit, but for some reason always reverts back to the default Safari favs over time, maybe like 10 links, none of the corporate links present anymore.

Am I missing something here? Will the Config Profile pushed via the JSS set some settings but will not set others? Does something else control the favs bar and the links there? The bar needs to show these links when the build goes out, and they need to stick. Any insight on this? As always, all help appreciated...

[htse]

i'm not sure how helpful this is, but this is a behaviour I've noticed in Safari, that spans versions. If you clear out the bookmarks, the default bookmarks will be restored on the next launch. You have to perform the action a second time for it to stay cleared.

[khenley]

I had similar issues applying changes to the Safari plist file but I was using a script of "default write" commands. I found that when Safari opens, a SafariUpdater process is started. Apparently it prevented my changes to the plist file from applying. Lesson for me was to make sure SafariUpdater is killed before trying to apply plist changes.