Yeah, that can be an occasionally dodgy combo--I use it myself every now and again.
A couple of things:
You might want to make sure all
the contacts inside the MD-12 and on the bottom of the FE are clean. Particularly if a battery has ever leaked inside the MD-12, you may have a bit of corrosion/oxidation in there. The best cleaning option is possibly one of those glass-fiber contact brushes (this
, or something similar). Or you could carefully apply a bit of Deoxit spray; just don't let it run down inside the mechanism.
Another thing, the motor drive occasionally gets out of sync with the state of the camera's drive train. Take the motor drive off the camera, and make sure the camera is wound on and firing properly. Then take a quarter and lay it across all four contacts on the MD-12 simultaneously, with the drive turned on. That should short the terminals and cause the drive to cycle, hopefully ending up in the proper position in the cycle. Then put it on the camera and see if everything is synced up.
And of course, make sure your batteries are fresh as possible. The motor draws a pretty high current when it's cycling, and batteries that may be perfectly fine for many low-drain uses may not provide enough peak current to get the drive to work properly snappy, which could lead to problems.
Finally, if none of the above works, chuck out your MD-12 and buy a new one. They're plentiful and cheap, no reason to get frustrated over one that's basically knackered.
My FE and MD-12 work together swimmingly more often than not, and when they do, you can definitely get your old-school photojournalist groove on. But having dealt with them myself, I know how frustrating the problems with that combo, when they arise, are. Hopefully amongst me and everyone else, someone will provide enough info to sort yours out.
By the way, if you love your FE like I love mine, one of my favorite tips is this: get you a K3 screen (intended for the FM3a) and put it in your FE. It's much brighter (you *might* have to adjust exposure a bit) and it snaps into focus much better than the original screen in the camera. Makes a pleasurable shooting experience even better.