Okay, I changed the condition to
if ((0 < cwTimeout && cwTimeout < millis())&&(isAM==0)
and was astonished, that this seems to do the trick.
However I do not know if this is recommendable or if this way any other problems will occur.
I will test it with the loop controller tomorrow, but I hope this works out.
I still don't know what the cause of the problem was, though I suppose now that it could be that the cwKeydown() function was started out of the cwKeyer function().
This could mean the cwTimeout never gets assigned the current time.....
Sascha