The Mac makes some assumptions about whether an OS is legacy or EFI. These assumptions can be overwritten by information that is stored in NVRAM (
source). Since you cleared the NVRAM, the Mac is going back to its assumptions, which are wrong for your setup.
If you just want to get back to working quickly, I think the best solution is to install
rEFInd to your OS X drive. As a side bonus I liked rEFInd much, much better than Apple's ALT/OPTION because it boots massively faster, you don't have to hold down a key, and it is deeply customizable. I cannot recommend it enough, in fact I would do this even if everything were working. It's just so much faster and better.
If you don't want a new bootloader, I believe
TwoCanoes WinClone can switch between legacy and EFI boot. I have not tried this myself.
If you want to fix it without going either the rEFInd or TwoCanoes route, I am not much of an expert on that but I can try to help if nobody smarter comes along in the mean time. Back up your important files first, LOL. Second step would be to install
EasyUEFI Free in Windows and post a screen shot of the Boot Order so that I can see what's going on.
