Hey, I'm having a strange issue:
I can place kerbals in the seat in the editor but they don't appear in game. It's as though they're inside the seat like a regular command pod, I can transfer them to other seats but they still remain 'inside'. They also don't count as a source of control for the vessel. Further testing showed that a kerbal spawned in a seat can be transferred to a pod and walk to the seat and get in like normal, even if there is a kerbal 'inside' the seat. Not sure how to insert images but it pretty much just confirms what I wrote out.
edit: nothing obstructing the seats, simply a structural piece with a command pod and an external seat with lots of space around each part.
Cheers.