I am running a Window XP Pro on my computer and I have 2 hard drives.

My problem is that my computer cannot locate my hard drive if I have spent a long time on some kind of big operation such as photo editing or deleting big files. I have to wait for at least 15 minutes before the computer is able to locate my primary hard drive on reboot or is able to locate my ohter programs on the hard drive (If I don't reboot). Do I have memory or paging problem or does my motherboard needs to be replaced,

Well many questions you asked and many answers can be gained.
Are they on same ide? If they are, is 1 a master the other a slave to the master?
If they are seperate ide's is one on primary master and set to master? The other on second ide and set the master also?

I have 1 hd set as master on primary ide 1. I have a dvd drive set as slave.
I have on other cable second ide a cd rom drive as a master. Now do you understand?

As for swap (paging file) I would allow windows to set it and set it to a small Partition.
I have total 527 ddr 333 r.a.m. which i set on a 1.5 gig spare partition 767-1267 for swap.

I also run xp pro sp2 build 2180.

There could be a clash, could be a 1001 things, list how your setup is. USB ports other devices such as dvd/cd rom drives, card readers etc that require such ports and cables.