If the problems came on kind of suddenly, run some malware scanners and I'm sure you'll find the cause.
Otherwise, it could be some errant program causing the problems, maybe you don't have enough RAM (512MB minimum for decent XP performance)... I've even had my boot times dramatically increased by an external enclosure.
There are no programs that are going to help you trace this, it's a matter of very tedious trial and error, plain and simple.
Are there any good diagnostic programs I can run to see why my computer is slow to BOOTUP and SHUTDOWN???? I'm not talking about programs like HIJACK THIS. I ran a program called PC DOCTOR that came with my computer and did a test on my hard drive, Memory and Motherboard and it passed all the tests.

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