The first thing I would look at is to see how many apps are starting when XP starts (Run>"msconfig" -- click Startup tab). If it is not this, then here are some other things to look at:
You no longer need a patch for larger hard drives so the drive thing is not an issue.
I am wondering about your memory. Do you have 2 sticks or 4, and is your configuration on Asus' acceptable list?
Do you have "quick boot" selected in BIOS?
Did you configure a 1-gig paging file, or did XP do that when it installed?
Also, can you more fully explain what is happening here: "reg file scanning programs really legit..."? What are you observing when this happens?