Possibly useful information about encoding challenges I have come across.

[630] NES Mike Tyson's Punch-Out!! "last boss only" by Mart in 04:50.40 and other MTPO runs made with Famtasia - I likely dumped these using FCEU 0.98.15, which can automatically convert FMV files using Nesmock.

[856] NES Shadow of the Ninja (Europe) by Xipo in 11:14.56 - You need to disable PAL mode to get this to synch. It seems like FCEU 0.98.15 enables PAL mode every time you replay or restart the movie, however, but it doesn't toggle the PAL Emulation checkmark in the Config menu if you disabled it previously. If you get a desynch on the character select screen, try this: Stop Movie -> Replay Movie -> Enable PAL Emulation -> Disable PAL Emulation. You could also do NES -> Power instead of the Stop and Replay steps.

[4195] Wii Namco Museum Megamix "Pac'n Roll Remix" by Elomavi in 15:21.02 - I used the following AviSynth function to replace frames that were dumped incorrectly, since they were all duplicates of a previous frame:

function DupF(clip c, int badstart, int "badend")
{
  end_defined = Defined(badend)
  removed = end_defined ? Loop(c, 0, badstart, badend) : DeleteFrame(c, badstart)
  duped = end_defined ? Loop(removed, badend - badstart + 2, badstart - 1, badstart - 1) : DuplicateFrame(removed, badstart - 1)
  return duped
}