Toolbox custom properties gone haywire!

Alrighty, a good place to start would be to detail some background before describing the problem. I will also go into the details that
probably aided this problem. (This is also posted on the SolidWorks forum, sorry if you read this twice).
Background All the toolbox parts what we use have three custom properties (CPs) that we created. There is Our P/N, Manuf. P/N, and Description. We've been using these custom properties for about 2 years without much problem. We're using SolidWorks 2007 Professional.
The Culprit? I updated us to SP4.0 (SW2007) from SP3.0 or SP3.1. I was thrilled to find that this erased all files on my server's root folder. Several days later my engineers informed me that the toolbox was messed up. I checked the custom properties of several specific parts (after rolling my eyes of course) and discovered that they were correct, something fishy was up with our toolbox!
Problem I had previously mentioned that we have 3 CPs for each configuration that we use. Now for some parts we only had two; "Description" was missing completely. Furthermore, some of my CPs had changed to the CPs of other parts. For example, my 0.25" regular lock washer lists the P/ N and Manuf. P/N of my 0.5" regular lock washer. Description was still missing, of course.
Plea Anyone who has seen similar funked behavior please let me know how you fixed it! I'd rather gnaw my arm off before telling my engineers they have to redo all these CPs, which would result in me watching them gnaw their arms off to avoid doing the same thing twice.
Thanks! The Mex
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