I upgraded Visual Assist from install 1246 to 1289 and have noticed that the Visual Studio.NET 2003 environment is even more sluggish than normal. Opening a project usually takes 5-10 minutes, starting a debug session takes several minutes, and after the app does some initialization it goes into an extended period of slumber that pratically halts the entire PC. I have disabled VA and have noticed that these problems still occur, but since disabling VA doesn't necessarially mean it's disabled I'm still skeptical.
I just got back from vacation and this problem could be caused by my no longer being used to the ridiculously slow pace at which Microsoft's VS.NET runs. I may need a few more days to get reacquainted with the molasses pace that Microsoft tolerates in their professional products.
I also resynched to a few additional days of code changes. It might be possible that bugs in our app is causing the system slowdown, but it wouldn't explain why it takes so long to start up Visual Studio and why it takes so long for a debug session to begin.