How much memory in your current system. If you have a gig or more its the page file. If you have alot of memory, you can reset the page file to a very small amount and speed that turkey up. additionally, how much stuff is in you startup? If you have a whole bunch of stuff running im memory it takes a long time to purge all those programs at shutdown. If I were you, I wouldn't have anything in start-up unless it's a critical windows app. Your just hamstringing windows.
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EVGA 680i, Dual EVGA 8800GT'S (650/950), 4 gigs OCZ DDR2 1066, Intel Q9450 at 3.8 Ghz, Koolance Water Cooled, Dual Plextor16x DL DVD+/-RW. Dual WD 250gb 16mb Cache Sata 3.0. 3DMark06 score = 19,168.