Last night I upgraded 3 Intel Mac Media Composer systems.  The 2 Macs that are running 10.5.5 had a funny thing happen. I upgraded from MC 3.1.1 to 3.5.4 and all went well except that the Dock was wiped clean. All application icons (including Apple's) vanished and we had to reload the Dock items when the editors came in this morning. The only items left in the Dock were Finder, Downloads, and System Preferences (which wasn't there to start with).The 1 Mac running 10.5.6 did not have this problem and it was also from MC 3.1.1. to 3.5.4.  Just an FYI.

-cable

There was a bug a while back in which the Avid uninstaller wiped the dock clean of most icons.  I think it was even pre 3.0.  Prehaps you had an old uninstaller on those systems?

I'm not sure the OS had anything to do with it, but maybe...

I thought that got fixed, but IIRC the solution was to remove the older MC icon from the dock before you did any upgrading.