Well I loaded up his savegame - He's playing the game with historical monarchs and such. I'm thinking that this is the cause of inability to be elected emperor of the HRE rather than some bug, as I can confirm that electors appear to at least vote for who they are listed as voting for in the HRE screen, even if they are otherwise pretty much broken.
Case closed I guess.
If you want to fix this, open your savegame file in notepad, and change the first three 1's in the game options section to 0's, like so:
Currently you have this:
It should be this if you want HRE elections to work properly, I think.
1 1 1 0 0 0 0 0 2 0 1 1 0 0 }
If this doesn't fix it post again and I will fiddle around some more and see if I can't figure out what is going on.
0 0 0 0 0 0 0 0 2 0 1 1 0 0 }
This should probably be added to the bug forum if this is the problem, though, as I can see how it may be misleading. If they're just going to vote historically (or if the historical emperor will be elected regardless) then they should either list the actual successor, not list anyone, or have a disclaimer in the HRE screen stating as much. Or all three.