A customer reported this problem. If you're seeing this, it probably means you forgot to install the April CTP. The problem is that the verson of Atlas that ends up in your bin directory doesn't match the one in your ..."program files\Microsoft ASP.NET\Atlas\v2.0.50727\Atlas" directory. Your project has a update pointer to the older version but gets the newer version in the bin directory and this causes compile times to slow down.
1) Make sure you've got the April CTP in the directory above (it should have a date of 4/7/06)
2) Delete the .refresh files from your website\bin directory