Had a similar problem with the German CAA(LBA) once...
Although they were granting me with the MCC-credit due to our military multi-crew-only operations (on Utility helicopters), they did not accept these hours as multi-crew hours for my ATPL(H) -conversion.
Even after i proved that i have flown the necessary hours according to JAR-FCL in a multi-pilot environment (according to the Ops Manual/Flight Manual)-including IR-they did not accept that.
I should have taken another checkride-ro be checked in a multi-pilot helicopter, thereafter starting to collect the necessary hours towards my ATPL(H) all over again...
According to JAR-FCL, you will need a multi-pilot type rating FIRST, before you can start collecting hours towards your ATPL(H) (as long as there are no other special agreements between your military and your CAA)...