You have to remember as LiteStep comes up it is loading all of the modules that you have picked. If you run a theme like Beetle2000, which jalist wrote waaay back when, you will wait hours. :) That theme runs about 30 modules on startup. You must also pay attention to what modules you are running. Some modules are written poorly and will just consume resources.

To find help in debuging your problem your best bet is probably irc and not these forums however. Hop on irc.freenode.net and give someone a hollar.