Are there any other high pressure signs (extractor / ejector marks, signs of case stretching, etc.?)
No clue what the cause is... but I can tell you what I would do to try to find the issue...
1) Pick one configuration of the gun - and confirm that it is in spec (check headspace / chamber - confirm with go / no-go gauges).
2) If you have a cartridge that you know and trust because you've shot a ton of it - preferably something that is a middle of the road cartridge - I'd take a box of it and tune the gas system to it as a baseline. Get the gun ejecting in the 3:00 - 4:30 ark and confirm no pressure signs, etc. If you DO have pressure signs or trouble getting the gun to group brass - stop and look more closely at the gun.
3) Given that it's 6.5 CM - not something obscure or super expensive - I'd buy a box of a bunch of different grades of ammo ranging from white box to good hunting stuff and including the Federal stuff that you are having trouble with - then get a chronograph and maybe a big tarp or two and go shoot it all. Record:
a) Velocity / SD / ES for each load
b) Where the brass is being thrown for each brand/load - direction and distance - take notes.
c) Pressure signs on the brass. If it were me - and I saw anything else go out of norm (velocity, or brass placement) I'd stop - and start recording each round individually and checking each case for pressure signs.
4) Compare your velocity data to both the box for that load - and to other similar products. Look for patterns - and for things that obviously break the pattern.
If you find that everything except the federal shoots fairly close to the advertised / expected velocities, and ejects in a pattern that is either "good" or perhaps consistent with what you are seeing in the velocity data - then you have your answer - it's the federal ammo. If you find that the negative signs are occurring across a variety of rounds - then look for the next pattern...
At the end of the day - the whole exercise is about changing just one thing until the issue is isolated.
Just my 2 cents.