Hi,
I did run top before, and nothing is showing up as chewing up CPU cycles. In fact most things are running at less than 0.1% during the startup of the application. When evolution finally starts, it increases to about 50%, while it loads all of the folder information.
The only real thing I noticed, is that no matter what I started "magicdev" seemed to kick in for about 2 seconds.
I have rebooted the machine without any difference. In fact it can be worse when you have just booted. Leaving the machine for about 1 hour seems to improve the overall performance of applications starting.
Thanks Matthew
If you haven't already, I would suggest running top to see if anything is chewing up CPU cycles. Pressing "M" will sort by memory usage, and you can check if something is hogging memory as well.
Of course, this is only a possible cause if your machine has been running for those 3-4 days.