In the last few weeks, 3 newly-installed single turbo n54s ran into a high RPM (~6500rpm) misfire problem. One local (tmo335tt) and two in florida. This came as a surprise to us given how many 6MT VFF single turbo cars are running around problem-free. We tried everything from updating DME software, revision CPS algorithms, changing torque limits/calculations in the flash, etc,. Short of disabling misfire detection in our flash (yuck), nothing seemed to solve the problem. We were working with tmo335tt for some time with this and it's a good thing that this problem happened to him because I don't think anyone else would have spent enough time figuring out the cause of the problem. Which he did.
The problem has to do with the factory dual-mass flywheel that twists at high torque levels. Combine that with high RPM (where misfire diagnostics is most sensitive) and you get a misfire fault without the real misfire. It also explains why the the only three misfiring Single Turbo 6MTs have stock dual-mass flywheels while all others have single mass lightweight flywheels. I also recall BMW themselves changing the clutch/flywheel assembly on the 1M for this reason. And that is only with a small power bump.
So no, the proper solution isn't to mess with the knock tables or to disable misfire detection (which I did today on tmo335tt's car until his new flywheel comes in next week). The real solution to run a suitable flywheel that is capable of withstanding the higher torque loads that upgraded turbos (and sometimes even stock turbos) are capable of supporting. Other option is to just make less power I suppose.
Hope that helps those 6MTs (like BigTom, IIRC) that were battling high rpm misfire. And big props for tmo335tt for wrapping his head around this and figuring this out. It will undoubtedly save a lot of people headache in the future as they try to make more and more power.
P.S. Here is some good info on the subject of dual-mass flywheels and misfire detection: