I don't know for sure if this is the root cause but I have seen this before and it was related to CEIP. The default start time for the CEIP (Windows Customer Experience Program) is around the time you are seeing.
On the systems experiencing the problem type this at a command prompt: (case sensitive)
CMD> schtasks | findstr Program
It may return the ProgramDataUpdater scheduled task at 12:30AM. There are several other tasks that run in addition to this one. They show up as SVCHOST. Check out this link to disable these tasks.
