We use the Air Video HD iOS app to connect to the AVHD Server to mainly just convert video on our media server which then gets added into iTunes so we can watch the content on Apple TV.
Recently (possibly since the new update) I've noticed MKV files taking upwards of 30 mins to convert, rather than less than a minute to convert previously.
I have noticed another post about the passthrough settings and I think I've changed them all in the app by:
1. In the app, selecting a Video file
2. Tap the (i) under the file title
3. Tap Conversion quality and set all to Preserve Original Tracks: Wherever Possible
4. Tap Passthrough Settings
5. Change/Ensure that: H.264 Video is Optimistic, MPEG Audio is Keep Original, MPEG-4 Audio is Optimistic
6. Direct Streaming (.mp4) is Enabled.
Back on the File Information screen, I tap the blue (i) next to "Audio track will be converted" and it shows that it will be "Keeping the original video track" and "Converting Audio track".
Yet when I go back to the file list and press and hold on the file and tap "Convert Only" it still takes 30 mins to convert.
I've tested by using WinFF with an MP4 Passthrough preset and it converts (remuxes) the video file in less than a minute, so at this stage I'm convinced that it must just be a matter of having some incorrect settings in AVHD after the recent AVHD update.