I can't see how connecting your linux HD has any bearing on the Vista boot, unless it's involved somehow in the boot process. The booting system shouldn't even know what's on there until you select Linux in the boot menu.
You need to investigate why the boot process is even accessing that disk.
If your BIOS sequence is as stated, the mbr on sata 1 should check which of V32 or XP64 is "active", and go to the boot sector of that partition, where it should find Vista's bootldr to execute. All of that should be quite independent of any other connected disk.
Is this a RAID array ?
If so, I have absolutely no practical experience of that and will leave it to others to sort out what could be the problem.