Yep, should be long end first - the nut halfway down the stud has a sort of built-in washer - that goes against the flange.
I snapped one off in my head as well, then managed to snap the stud extractor in the remains of the bolt! ended up drilling out and helicoiling the b*gger to get the flange attached.
You've not got the remains of a bolt or something wedged at the bottom of the hole have you? check the depth by shoving a bit of stiff wire or something in there and comparing it to the length of the bolt...
If there is it might be worth chopping 5mm or so off the new bolt (spin a nut on first so it cleans up the thread as it comes off again) and see if that gets you anywhere... as long as the thread at the top of the hole is good you should be OK.