Slow HDD access at times

Hi there, heres my system:

2 x 1TB Western Digital WD1002FAEXSATA 6Gb/s drives (1 of them partitioned in two with OS installed)
1 x Samsung SpinPoint F1 HD753LJ 7200 32mb Cache SATA II

Gigabyte GA-X58A UD3R Rev2
Intel Core i7 930 - Quad Core & HT CPU
6Gb Corsair XMS3 DDR3 1600Mhz
3 x SATA II CD Writers
Corsair 650W PSU
Windows 7 Pro x64

Now, It might be just me but lets say I’m doing some intensive hard disc bashing (like copying files) - the PC becomes slow to use and even simple things like loading a web page takes noticeably longer. Surely thats not normal? Could the drives be incorrectly set up or a driver issue? Could the drives be faulty? Running in AHCI (but  IDE mode also the same) and no Raid and all the latest motherboard drivers installed. Any ideas?