[underworld123]

In Handbrake.

Container: MKV
Preset: High Profile

Under Video
Video Codec: H.264 (x264)
FPS: Same as source
and select Constant Framerate (leaving at Variable Framerate may cause issues with some vids, even though "Same as source" encodes it at the same fps as the source whether it's set to variable or constant.)
Quaility: 20 RF (for BD) 19 RF (for DVD, but you can set also for BD)
(Don't go any lower than 19 RF, you want see any improvement in playback)

And if your using HB 0.9.9 or nightlies
x264 Preset: Slower (or lower)
x264 Tune: None
H.264 Profile: High H.264 Level: 4.1

Under Audio:
Use the AC3, DTS or DTS-HD MA tracks and set to pass-through (same as source, i.e. AC3, DTS, DTS-HD MA)

Leave everything else as is.

Thanks! If I inderstand this correctly, we are not changing the audio (assuming that audio is not a problem on fire tv) and only encoding the video so that it plays correctly (as video is the source of all the issues)