When I try to boot into Windows I get 'Invalid EFI file path'. I can still get into Windows by going into BIOS and making my other hard drive the boot priority, which is a pain.
I've since installed Windows 8 and the issue is the same.
I just ran Boot-repair and this is the output: http://paste2.org/p/2726047
It also says something like 'unable to find command DRIVEMAP'. Which it did not a couple of weeks ago when I first had the issue.