This thread is a compilation of my findings from https://jamfnation.jamfsoftware.com/discussion.html?id=14003.
I have confirmed that either installing the 10.10.3 combo update via Self Service or running Software Update via Self Service coupled with the "Reboot Immediately" items WILL NOT reboot the machine, and results in a barely functional machine until a manual reboot. No bundled apps will launch, and any you try to launch will prevent a manual reboot until you force quit them. I also tried adding a /sbin/reboot command to the combo update policy, and it does nothing. I have also tried the non-combo 10.10.3 update with the same result.
Running "softwareupdate -ai” locally on the machine via terminal produces the exact same result. While this method does grab the updates and installs them, once its finished and gives you the "You have installed one or more updates which requires that you restart your computer...", if you don't reboot and try to launch any of Apples included apps or utilities, they never launch and must be force quit before you can manually reboot.
Right now it looks like the only valid method for updating to 10.10.3 in a manner that works as expected is to do it via the App Store, where it will download it, prompt you to reboot, and does the install at the Software Update screen post-logout.
Any thoughts as to what could be causing this? We really need to be able to point people to Self Service for updates as we have done in the past. Our branded Self Service app is front and center in terms of the Mac Teams visibility, and not being able to use it for the 10.10.3 update breaks our successful run of offering both specific OS updates and being able to kick off Software Update. If we cannot fix this we are going have to disable all Self Service based and Push based Software Update policies for 10.10 machines in the JSS, and hope that users will go to the App Store and install the updates from there.
JAMF confirmed this - "SWU policy with 10.10.3 hard freezes Mac at policy completion" (D-008920)
