Ok first off, not sure what you mean by the purple and yellow connector, are you talking about SATA cable colors? If so , that's meaningless. If you mean GSATA ports on the MOBO vs SATA ports, then read the MOBO manual about the difference btwn GSATA ports and SATA ports.
Are your HD's SATA or IDE?
DO you have IDE controller enabled in your BIOS?
I'm getting that you have win 7/win xp installed on the 250gb HD and Win 7/ubuntu on the 1TB and no OS installed on the 160gb.
If yes, then just reformat the 1 TB.
In addition, in a new system, when you install an OS it looks for other OS on all HD's and will add them to the boot list. If you used preinstalled OS drives then they will not know about existence of other OS's.
If you're combining multiple HD with OS's on them, and they were not installed onto the HD's in the final system, you will have issues.
Also, Vista and I think it was carried over to 7, use a separate boot loader than XP so, XP must be installed first before Vista/7. In addition Ubuntu might have issue which you'll have to look up.