Working on deploying 9.5 SP1 and I've noticed the servers generate a new ID for the new software groups (now package groups) that are desginated from that server... We use autosync to copy packages among the cores from a master core. This is causing multiple copies of the software groups to be made and place tons of linked packages everywhere.
Another problem I found was some packages report they are linked as a dependant package to another package when you attempt to delete. Problem is, the package isnt really dependant on the one in the error. (Example: Try and delete application X, presents an error saying you cant because package Y depends on it, application X only has package B as a dependancy not package Y).
Has anyone else experienced any issues similar or have suggestions to resolve? I'm in the process of re-syncing the packages to copy over the correct group IDs.