slow system with heavy cpu use

ok, system Mainboard : Abit AX8 Series(VIA K8T890-8237),Processor : AMD Athlon 64 3000+ @ 1800 MHz,Physical Memory : 4096 MB (4 x 1024 DDR-SDRAM ),Video Card : NVIDIA GeForce 8400 GS ,DVD-Rom Drive : HL-DT-STDVDRAM GH22NS50 ,Operating System : Microsoft Windows XP Home Edition 5.01.2600 Service Pack 3, i have a 500gb wd caviar hdd for XP boot, i have a 1tb sata hdd for 2 boot drive to install vista awaiting 7 upgrade on(so i have installed XP on it first then next to vista & then to 7,but not there quite yet), so when i installed the second drive, to install the os (XP), and then finished, now then to reinstall first drive-500 gig hdd(which was first drive in system) i'd not installed it in the same order- sata one, so i had sata port 1- 1tb drive , 2 sata port for the dvd rw drive and the 3rd sata port with the first 500gig hdd, when i started the system up and allowed it to load, the os loaded slowly, and then when anything was opened, it would command 80 to 100% cpu load. i found this to be true using the windows task manager and watching the cpu load. the system would freeze with almost anything opened or more then one program running . ok, i removed the second hdd( the 1tb) and rebooted, still same thing, so then i took the sata cable from the 3rd port and put it in the 1st port and then it works fine, that is with only the hdd and the dvd rw installed in sata ports one and two, normal operation. the question- is there a "port order", if i'm trying to have a dual boot system will i have to deal with it being slow?-not likely, is there a bois update to fix it? or am i supposed to have a raid array - which i DO NOT understand how it works for a dual boot,
p.s. i had this set up (dual boot) with the last system i had , but, it was an ide drive system. and lastly in case your wondering, the dual boot was 2 drives loaded with windows XP as main drives then when i wanted to change drives i just changed the boot order in the bios. thanks
jrc