I have very little long haul experience of KLM. But I have a lot with BA.
When BA introduced the 747-400, it had lots of problems with it on long haul flights.At that time I was "commuting" to Singapore. Due to the problems with the 747-400's introduction, I was 1. Very late in to Singapore, 2. Flown to Athens, instead of LHR, flown to Schiphol instead of LHR, flown by SQ to Manchester, instead of by BA to LHR.
Eventually, they sorted the problems out.
Maybe your issue was just KLM's version of BA's struggles?