Hi Paul,
I'm glad it helped. Actually I must correct myself - I believe 100 sec timeout is only for Linux. For Windows it seems like it can actually run indefinitely. Anyway, in your case the PowerShell script seem to quit earlier than it finishes all the tasks. And we reboot once we see the script is finished.
However, I'm now wondering about another thing. You run VCD 5.1.1, but is it upgraded from 1.5? The reason I'm asking is that you may be hitting another issue and still using 1.5 customization code (because of cached package files).
/Andrii