Help. Black flashing cursor at boot when external HD attached via thunderbolt?

I installed windows 7 via bootcamp today on my primary SSD with high hope that the thunderbolt port would help with my limited space, however I have ran into an issue.

What i'm using:

• MBR with Retina display
• Thunderbolt Cable from apple
• GoFlex Thunderbolt Adapter + Seagate Drive
• Lion OSX

I've succesfully attached the drive/goflex and can see the drive on the mac using the disk utility I can also drag and drop files too the disk. In windows i can use the thunderbolt port with my gigbit adapter and with my firewire adapter. The only issue occurs when I try and boot the system with the thunderbolt cable attached to the goflex, i get a black boot screen with a blinking cursor.

Ive done alot of messing around and all i can think of is that when the system is booting its trying to boot the thunderbolt drive before the windows bootcamp partition.

Any thoughts on how to solve this would be greatly appreciated.