ATA-100 drives will slow down when transferring. I will look into it more but i need to get some sleep. I will be back in about 9 hours and see what I can come up with. I think the problem with the information you just provided is the transfer rate as the system seems to work good otherwise.
The option is to upgrade to a faster hd or a newer system
The second option is better for you because you can go to the newer SATA drives which are much faster and cheaper then the IDE drives you have now.
You can buy a nice system for about 300 dollars now with a 250 gig SATA drive and still keep your larger second drive if you would like to use it.