Background: I had been using Slacko 5.3, and found on moving to 5.4 that the periodic saving to savefile process took absolutely ages. Sometimes it would use 100% CPU for over 2 minutes.
I reinstalled using the PAE build and the problem is cured.
Since my savefile was 4GB I think that the problem was that if you want to have a 4GB savefile working properly you have to have the PAE drivers.
Just thought I would post this as I know a couple of other people were having the problem.