Hi Daniel,
Do you think that this is could be related with probes itself?
Well, seems I did pretty stupid testing, but I tried to logging temperature inside BNC connector.
I used my Fluke 287 with thermocouple probe putted inside BNC itself, because probes end, close to BNC seems to be "slightly" warm. This is chassis warm up, and to be honestly, I do not believe that passive components inside probe can be such unstable with 5-10 C degrees warm up.
After 5 min rest thermocouple probe inside the BNC (just to check that temp is stable), I turn on power of my scope. As you can see, temp was rice more than 7 C degrees at 25 min, after that thermocouple has been extracted.
At beginning, probes also seems been undercompensated, but with warm up it been more and more close to past fine compensation. After one hour probe connected to Ch.1 seems been fine compensated.
Well,.. I connected second probe, that rested on the table before, at Ch.2 BNC and after 15 min in seems to be approaching to Ch.1
I do not know, is it really make to sence, but hope it will help (if your team really see problem. Just may be all this does not matter for scope work)