emulatorII-list

I can't exactly diagnose your problem but I've had many problems with my set-up and now 
it's working so I'll just share my configuration so you can try it.

Apple talk off
Printer port selected within SD
Mac > printer port > EII

From time to time I get the "I can't communicate" message but if I try to send the bank 
again straight away it works.
Disconnect your midi cables while your still testing.  You can put them back once 
everything is working.
Remember, these are stubborn, fickle old machines - sometimes if you just keep trying 
they'll start working.

Lastly, count yourself lucky you don't have my set-up:  Oberheim OBXa, Arp Odyssey, 
Emulator II, Roland Juno 106.  They are the bane of my life and a CONSTANT source of 
problems.  That said, I would never exchange them for modern equipment.  Even if some 
days I feel more like a studio maintenance technician than a musician!

Good luck,
Martin