Sounds like the BIOS is changing the 'Drive Id' of your boot drive when the other disks are installed. Here's how it works on my PC.
If I have only 1 disk and it is connected to SATA 1 it has id = 0.
If I have 2 disks, one disk in SATA 1 and one in SATA 2 they have id's of 0 and 1.
If I have only 1 disk and it is connected to
SATA 2 it has id =
0 !
The assigned disk Id is important. During the startup process your boot drive uses this Id to identify the drive that contains the actual OS files, under XP this information is stored in the file boot.ini, Vista/Win7 save the information in the Boot Configuration Data (BCD) database (guessing here

).
Back to my PC and a typical boot disk created when it was the only disk on the system and therefore contains the information 'disk Id 0 contains the OS files' ...
If I have only 1 boot disk and it is connected to SATA 1 it has id = 0. System boots.
If I have only 1 boot disk and it is connected to SATA 2 it has id = 0. System boots.
If I have 1 boot disk connected to SATA 1 (id = 0) and 1 data disk connected to SATA 2 (id=1). System boots.
If I have 1 boot disk connected to
SATA 2 (id = 1) and 1 data disk connected to
SATA 1 (id=0). System fails to boot! Disk id=0 no longer contains the OS.
If I have 2 identical boot disks... Lol, try it yourself one day
If I had your problem on my system I'd ensure my boot disk was connected to SATA 1 and that would be an end to it - all additional drives would be assigned ID's from 1 and upwards. On your system, especially if your motherboard has 2 or more SATA controller chips, things may be more tricky. Check your BIOS and the manual to see how the MB deals with/assigns disk Ids to the SATA ports.
G'd luck