Wondering if anyone has seen this issue.

I have one particular Windows 7 VM with Designer installed in it (currently at 4.6.1) and I have a project in there that when I modify policies and do either a deploy or compare, Designer says they are equal when I know darn well they are not. The only way I seem to be able to get Designer to detect the change/difference is to close the policy and re-open it, then it detects the differences and deploys properly. Other VMs and instances of Designer I have no issue at all. It's only this one instance. Has anyone ever seen this before? It's getting really annoying to have to close the policy and re-open it for every little change. I'm wondering if I messed up some setting in Eclipse or something somewhere when trying to tweak performance. But I'm not sure what to check. Any ideas??