Slow XP on new hardware

A year ago, by P4 died. Went out and assembled what I thought would be a solid machine. I'm not a gamer, but I wanted a machine that was responsive and very stable. What I ended up with was a machine that is pretty solid, but much slower than my previous machine.

Current machine:
Gigabyte EX58-UD3R mobo
4 GB RAM
2 TB HD (RAID 1)
ATI AIW HD video card
700 Watt PS

What I should mention is that I am using an IDE drive to boot the computer and using my 2 TB SATA drive for storage. At this point, I'm guessing that the IDE drive may be slowing things down a bit, but I was using IDE drives on my last computer which ran much faster than my current system.

I've tried reconfiguring the system many times (basically, doing a complete format and reinstall of OS and drivers and then adding basic software). I have not pinpointed where things go south, but the more "things" I do on the system like enable RAID or load some basic software like Firefox or Outlook, eventually, I end up with a very slow system. Especially at start up, it'll take several minutes for XP to become responsive. So with kind of the bare essentials loaded, I have a slow system - nothing extreme here at all.

What I have noticed several times over the last year (and it has happened today which is why I am posting this message) is that if I am on my computer working for the entire day (say more than 6 hours), I suddenly have a machine that seems to be working as it should. It becomes very responsive and acts like a machine that has the sufficient power to make things happen. And you may just think like I did that eventually everything gets loaded in memory over time, so that is why the machine becomes more responsive. But even when I load something that I am sure I haven't loaded before on that day, it comes up quickly. And when the machine is not responsive, loading the same program like IE seems to take forever.

So I'm baffled at this point. The machine is pretty stable otherwise and only crashes when I try to run the ATI catalyst software which has always been an issue on every machine that I have owned.

So if anyone has any ideas, I would greatly appreciate some insight. So the longer I use my machine, the faster it gets - isn't it usually the opposite?