After much research I found a workaround. We copied the csv file to the exchange 5.5 system and imported it manually. After this the connector wizard was happy.
We still ran into a problem in the next step but I could find information on it. The NT 4.0 server running exchange 5.5 wasn’t set to use lmhosts or DNS for netbios lookups. I added the 2003 server to the lmhosts file, told the server to use it, and for good measure told it to use DNS for netbios lookups as well.