I've noted this behaviour in my 2009, 2010 and now 2011 models. Now, the fact is I put the OptiBay in meaning that I wanted to boot from an external USB - I think this is why the assumption is it's something to do with the OptiBay.
It isn't.
My 17" 2011 MBP is sitting right here OptiBay less with it's normal SuperDrive in place - and guess what, I still can't boot from any of the my 3 external DVD drives. It's nothing to do with the OptiBay.
Thing is, if you don't have the OptiBay in why don't you just boot from the internal SuperDrive......
I feel your pain, it's really frustrating. If I want to put a fresh Boot Camp build on, or even boot from the DVD to run any utlities I have to strip the machine down and put the SuperDrive back in.
I think the OptiBay is effectively a red-herring here. It's not causing the problem technically - it's irrelevant from what I can see. Well, unless you accept 'causing' to mean putting the OptiBay in 'causes' you to remove the DVD drive 🙂