3) Did you look at whether the Onkyo's own lip sync settings are set to zero. If they are not, you might see lip sync issues. where will I find this setting?
Wow your NR929 has a lot of settings! (that could be a blessing or a curse).
See page 79 of the manual
http://www.eu.onkyo.com/downloads/2/5/1/7/3/Manual_TX-NR929_En.pdf (download and save a copy to you computer for quick access).
It says (under Hardware Settings):
■A/V Sync
0msec to 800msec in 5 msec steps
When using progressive scanning on your Blu-ray
Disc/DVD player, you may find that the picture and
sound are out of sync. With this setting, you can
correct this by delaying the audio signals.
Press ENTER to view the TV picture while setting the
delay when the video source is output to HDMI OUT
MAIN.
To return to the previous screen, press RETURN.
The range of values you can adjust will depend on
whether your TV or display supports HDMI Lip Sync
and if the “Lip Sync” setting is set to “On” or not
(➔ page 79).
then, see ■Lip Sync
Off
On
This function allows the AV receiver to automatically
correct any delay between the video and the audio,
based on the data from the connected monitor.
Note
• This function works only if your HDMI-compatible TV
supports HDMI Lip Sync.
I see your Onkyo also has a film mode setting (page 74). I don't know if this will help or not, but I would set it to AUTO.
■Film Mode*2*4
Video:
“Film Mode” detection is not applied and the
input signal is handled as a video source.
Auto:
Detects whether the input signal is a video or a
movie. If it is a movie, the appropriate
conversion is applied.
The AV receiver will adjust to the picture source,
automatically converting it to the appropriate
progressive signal and reproducing the natural quality
of the original picture.
4) Finally, is that 25 fps mp4 really 25 fps? Does it fail to play when set to 50Hz? Isn't your desktop at 50 Hz, and if so, there may not need to be a change if refresh rate when playing 25 fps material desktop 60hz goes funny when trying 50hz video fails when set at 50 or 25
If you look at the FPS tag in JRiver MC and it is set as "25" but you find that the movie plays much better when the fps is set to "24", I would then change the FPS tag in JRiver to the setting where it plays best. It is entirely possible that the file has the wrong tag from wherever it came from - or maybe JRiver is messing up the fps tag data when it is imported into your library. The safest way to know how your Onkyo and TV are working is to play a Blu-ray movie from a stand-alone BD player. Then if it plays nice and smooth you will know that the TV and Onkyo are setup correctly (and can turn your attention to your "ripped" movies and/or the MC settings.