Are you running multiple operating systems? LIke one on the sata and one on the ide drive? If so then while you have one of the windows running go to - Start, Run, - type in "msconfig" and click on the boot tab." Look to see which operating system is set to boot first, change the order if necessary. Or you can delete one from the boot menu then only the one left will start.
Otherwise your saying that when you go into bios, you are actually changing the order of the drives? Not just hitting the F12 key to boot from a particular drive? Then doing the save and exit? When you reboot and go back into bios it remains in the order you put them? Stays that way no matter how many times you reboot and start windows? Then, when you shut down for any length of time it reverts back to the old way? Which drive does it keep returning to? The sata or the ide? Check, while in bios, can you remove/disable all boot devices except the one you want to boot from most of the time. Then, if/when you want to boot from a different drive you can go to the F12 and select the other one on those rare occasions when you want to boot to the other drive. Sorry for the stupid questions, just trying to wrap my head around it.