When searching for a move suddenly the number of processed nodes was different, different pvs were calculated and sometimes also different best moves were returned. So I knew there was a bug some where but it was very hard to spot as both programs just for themselves appeared to run fine.
I reversed recent code changes to spot the source of the error but it did not help, both versions behaved differently, so I started the bug hunting session. Errors produced by the search algorithm are very hard to spot because the algorithm is recursive and calls itself several thousand times a second. I finally was able to spot the last position were both programs were equal, so I knew this position was somehow the cause of the problem. It showed that eval returned in both executables different scores for that position. From now on it was easy as eval is not recursive.
The root cause was an array with pawn bonuses per rank. The array was sized too small. In some positions the access to that array just exceeded the bounds of the array and retrieved a random number that just happened to be at the memory position. This random number was not the same in the MSVC and the gnu version and so the execution started to run differently.
This was then a quick fix and now both versions are consistent again.
I ran a quick tournament (50 games) of the latest ice version against a former not too old release to measure whether recent changes improved the strength of the engine. And the latest release scored
38 : 12
So although I consider the engine rather weak at least there seems to be some progress.