Are both of these installs on the same hard drive? Davehc brings up you may have separate BCD stores for some reason. You might check if bcdedit produces different results based on which OS you boot into. Since there can only be one active partition on each hard drive, and you cannot have duplicate folders, it does not seem likely you could have this situation on one drive.
You might also set your system to view both hidden and system file and look for a
Boot folder. This is where the BCD store is kept.
Maybe a picture of your Disk Management details would help. You can use the snipping tool to take the picture and attach.
I do notice two things which mean you are familiar with the boot system. You do not have the System Partition Windows 7 normally installs unless you pre-format the drive and you show a "do not show boot menu" entry in the BCD store.
The only other thing I could even imagine is that somehow the bcd store has become corrupted and replacing it as you tried did not actually remove the corrupted one. Or the boot manager is directing you to another boot menu
To replace the boot files, you can use the
BCDBoot.exe utility.
A command to replace the store would be:
bcdboot C:\Windows
Have you used any other OSes on your system that might have left traces, and are you sure the boot menu you are seeing is a Windows 7 one? Any External drives installed?