I have a bunch of DVD's encoded as mp4 files and have been attempting to find the best solution to play them on the Roku. Over the network I have tried Chaneru and Roksbox. Locally, I plugged a USB stick into the Roku and played a file through the new USB Media Player. In every situation the audio is not synced up to the video. It seems that it is about a half of a second off.
All of the videos were encoded with Handbake at the "High Profile" setting. I tried a different encoding putting the FPS at 25 as opposed to matching the original source on my first encoding. The videos play fine through my Xbox over the network using Tversity as the media sever.
Last night, I encoded a movie (from a raw rip) at 29.97 FPS. This morning I played it on the Roku from a USB flash drive and I still had the audio sync issue. Maybe I will try encoding at the other lower FPS you mentioned but I'm guessing that if it didn't work at 29.97 then its not a FPS issue.
I thought for sure the fps setting would make a difference. I agree, if 29.97 didn't do it then 23.976 probably won't either, but it's still worth a try. I've converted lots of videos with HandBrake, but only a couple of ripped movies. I don't remember any problems, but I probably haven't even watched all of the few I've converted. I assume you're not seeing this problem with Netflix movies? In other words, it's not something with the way you have the audio connections setup or routed through some kind of audio processor?
As we suspected, the 23.997 frame rate did not fix it either. I also tried a different encoding using AAC passthru audio but still had the same results. My next guess is maybe the deinterlace or decomb setting (both of which were turned on). Answering your previous question, no, I do not have it going through a complex audio setup, just an HDMI straight to my audio receiver. We watch a lot of content through Netflix, Amazon, and Hulu Plus but I have never once had the same issue with those channels.
The thing that is frustrating is that it has to be some limitation of the Roku box. If I play the same files on my PC or Xbox I do not have any audio sync issues. I'm really surprised that no one else has had similar problems playing files back on their Roku.
To continue testing, I may just encode at all of Handbrake's different profile settings, see if I can find any difference and that might help narrow down a setting.
I think I have found a solution. I encoded the same movie at different Handbrake presets and then played them all on the Roku through a USB flash drive. The "Apple TV" preset presented no noticeable audio sync problems with the video. I plan on encoding a few more movies on this setting and if I find anything different I will post the results here.