Two SATA Hard Drives, Main Drive only shows up in Bios if PC is off

I am having a devil of a problem.  My main hard drive is a SATA Seagate 500GB, my other HD is a STAT 80GB that I use for a scratch drive for Photoshop.  When I boot from the PC being off, the MB recognizes my Seagate 500 Sata HD.  When I reboot, it cannot find the 500 GB and I get the NTLDR is Missing message that system files aren't found.  This occurs no matter how often I reboot.
I have swapped SATA cables on the drives and that did not make a difference!  The cables are securely connected, as are the power cable.
XP Professional SP3, latest updaates
K9A2 Platinum Ver. 1, Bios Ver 2.8.1030.0032
AMD X3-720, 4x 1GB- OCZ Platinum Ver 2, 8500
Ultra 700w power supply
Fastrack - what does it do?

"It is the Promise RAID controller, that controls SATA ports 5 & 6. If you're not using them, you can disable the 'Extra RAID Controller' in BIOS (under Integrated Peripherals)"   
I am u7sing the 5th SATA slot for the extra esata pieces.  I will turn them off.
"Did this system ever work?
What did you alter before this happened?"
I replaced the CMOS battery.  It was dying.  I checked it on two separate battery checkers.
"Looks to me as if Windows has messed up partitions in some way.
Check the following, please:
- is the Windows disk set as frst boot drive in the bios?
- Is NTLDR actually on that drive in the root? (You must let Windows show hidden/system files).
- Is the drive detected by the bios at a reboot? (Does it show in the POST-screen?)"
Floppy Drive first, then CD-ROM (Sata), then the Seagate HD.
NTDLR is on the drive in the Root.  When it recognizes the drive and boots from it, it is fine.
No, it is not detected at a reboot.  It does not show in the POST screen.
"You have a Q-Tec Power Supply? Change that first and come back later... "
Is the Ultra brand Q-Tec?  It has a lifetime warranty...

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    Launch the Terminal application in any of the following ways:
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