We just found out that the defined MTU's differ, and I always heard that MTU 
sizes should be identical:

Unless path discovery is active on both ends of the link, the sizes should be 
identical.

Might this be an explanation?  How comes it works fine (most of the time) with 
apparently different MTU values?

Nothing sent a packet big enough to cause one end to need fragmentation, so you 
got lucky. It broke when you got a very large packet that needed to be 
fragmented, Path MTU discovery was off, and the sending side kept trying to 
send and got rejected.  Since you're running DRDA, that would be an easy 
scenario to do, since the results of queries would be different sizes.

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