If you don't shut down properly, then the startup process will take longer, since there are some extra checks that the OS does to make sure the disk and RAM, etc. are OK.
Are you having sleep problems, perhaps, when you put the PB to sleep but then the battery runs out prematurely and you have to restart the next time you plug in?
In addition to zapping the PRAM, I would reset the Power Manager, too. Unfortunately, each model PB has a different way to reset the Power Manager. Search Apple's Support site to find the way to do it for your PB.