Chaintech 7JNL6 and SATA HD

I've have an issue, not sure what to do
I have a Chaintech 7JNL6 with an AMD XP 1300 I think, I'll have to double check that one.

I installed a new WD SATA HD, during the setup process for the drive it asked if I was going to use this for storage or a boot drive, I wanted to use it for a boot drive, replacing my IDE drive, I didnt realize it would mirror the old drive to the new one but when it was done it reboted and everything seemed fine.
Every once in a while when I start the system up it wont boot to windows, it starts the usual processes, then goes to another screen with Realtek boot agent, it says it's searching for an array
then after a few seconds it restarts and just keeps looping.
Every once in a while it will go normally and get to windows.
I believe I've got the bios setup correct, I've enabled SATA, not sure if I need drivers or not. I'm wondering about flashing the bios but I don't have a floppy in the system, could I use a USB thumb drive?

I still have the IDE drives plugged into the MB, during the startup the bios does not see them, I've heard that the 2 wont play nice together, could that be the issue?

Thanks

everything is hooked up correctly.