There are far too few details in your post to guess what it could be. To start figuring it out I would use tools like your know about but here's another.
Look at the tools they used to find out what it was. Now go use that.
My system is a 7 year old Compac Presario with 512mb RAM and running XP SP3.
I have been trying to improve my computer startup time. I have done the the recommended things that I have read about such as disk cleanup, disk defragmentation, delete unnecessary items on startup tab, etc. These helped some. It now takes about 10 minutes for the computer to stop running (no disk activity) on the initial startup of the day. For subsequent startups on the same day it takes only 4 minutes. This led me to a file C:\WINDOWS\WindowsUpdate. This is a text document that has many entries during the startup times - 130 for the initial startup, 50 for the subsequent startup.
Can anyone tell me why the startup times are different?