We went through a period where that happened to us a lot. I think it was when we were doing a lot of name mapping at once. Seemed like TestComplete would just get tired and quit reading the mapping and then we would start seeing the Windows info instead of the mapped names. We tried to track it down but it was taking too long and we couldn't reproduce it at will, so we just learned to reboot when it started happening because it was going to crash eventually and that was the quick solution. Haven't seen it in a while, but we've been working with the same name mapping for several months.
Another note, when TestComplete is running slow for us, we can open the mapping for an object and see the Windows info fill in and then switch to the .Net mapping. I'm sure that we just don't see that happening when it's running at normal speed, but that may lend some credence to your theory about the plug-in.