I can almost guarantee that it will be a lack of a memory and cache config .h file, or an incorrectly set up one. Shake really needs it. They reinstalled shake in one of the suites I use and it was running like a dog. It took me ages to realize that my config.h file had been trashed. I was getting what were 6 second frames coming in at 380 seconds!
grab the shake configurator from the tools section if you, like me, are sketchy on what values to put in, but it makes the world of difference.
Cheers,
Toby