My wife is croatian with a C-Permit. She has not quite yet changed the name on her C-Permit or her Passport. (marriage is 3 months old)

However, now her employer is asking for her new C-Permit. She went to the Gemeinde and they said they wouldn't change it, until her passport is changed. Has anyone had experience with traveling a passport that has a different name than your C-permit.

When I was in a similar position I had to show our certificate of marriage (we have a multilingual version) at the airport and there weren't any problems.

Yes.....but it happens very quickly so unless you travel VERY often, it shouldn't arise. Change the passport, then take it to the Gemeinde......we got ours back with the new name within 48 hours