Thomas,
The bus extender is not truly "transparent". In actuality, it acts as a GPIB repeater. The extender will essentially listen on every GPIB address and repeat the same data and command bytes out the other side. So, when you do a scan for instruments, the software will detect that there are 31 listeners on GPIB. The bus extender should however, be transparent to an application that does not make usage of FindLstn or ibln functionality.
You may want to develop your application connected directly to your instrument, then go ahead and insert the bus extender. At this point, your application ought to work the same.
I hope this helps out.
Craig A.
National Instruments Engineer