Unfortunately that isn't much to go on, but I would say give the OS a few days of normal use.
While those times to display a window are too slow, when Windows 7 first starts it begins indexing the FS and determining how to cache your applications, both of which can be expensive operations to setup.
It's possible you became used to the pre-fetching and indexing of your previous installation which resulted in the perceived performance gap.
If it continues to be a problem, you can use the perfmon counters to see if you may have a HDD bottleneck. Was it an issue opening an explorer issue that one time that took 10 seconds, or is it fairly consistent? Was it while you were installing GTA IV?
Finally, the Windows Experience Index numbers may change a bit on subsequent runs due to other things going on the background and they are only a rough benchmark at best.
If the one thing you did differently was installing the HD6850, I would ensure that you have the most recent drivers from AMD. I'm not sure where the GPU fit into your series of events from your post.