As discussed on the Tools page, MP4tools is an Objective-C application that acts as an interface for a number of UNIX command-line applications. So if you encounter problems with MP4tools, often it's an issue with one of the UNIX applications.
To help evaluate causes of strange behavior, you can select to keep the log files that are created during processing. This option is found in the MP4tools preferences . Examining these log files should give you some hints regarding what the Unix applications are having issues with. The web sites for the individual Tools could also prove helpful.
Probably the best resource would be useful Mac video forums found here or here. You'll find lots of people there willing to help and with more knowledge about general video issues than I have. Also, I periodically read this forum and can chime in with specific MP4tools issues.
- Videos played in the newest update for Apple TV (6.1) stutters during panning: This seems to be a Apple issue as the same files played fine on other iDevices and older versions of Apple TV OS. For now, there is an option in MP4tools what will remux the video with no quality loss that seems to fix the issue in most cases.
- The output video is missing, smaller than it should be, or is not playable: Some error occurred during processing. Check the log file(s) that should have been created (if keep log files is checked in preferences) for error messages.
- Muxed subtitles are missing from the output: Only text-based subtitles can be muxed into MP4/M4V videos. PGS and VOBSUB subtitles are graphical, and so can not be muxed by MP4tools, though they can be burned. If you have registered SUBtools, you can send the graphical subtitle to that application, which is able to convert it to an SRT subtitle and sent them back to MP4tools to be muxed into your video.
- Burned subtitles are missing from the output: When burning subtitles, the video must be re-encoded. Though MP4tools will allow it, the passthru option is in red to warn you against selecting it when burning subtitles.
- Two sets of subtitles appear in the output when burning: When burning subtitles, MP4tools may need to extract subtitles from the file. When you play the output video, some software players will look for external subtitle files with similar names and assume that they should be played with the video. So on playback you will see the burned subtitles and the text from the external file. Deleting the external file should fix this.
- Burned/muxed text-based subtitles contain strange characters: This is most likely a text encoding issue. For best results, the subtitle file should use UTF-8 encoding. If you have registered SUBtools, and have set the output text encoding to UTF-8 in its preferences, a quick way to ensure a proper text encoding is to the send the subtitle to SUBtools, and then send it back to MP4tools. The text encoding should be properly set in the new subtitle track that will appear in the track window.
- Quicktime/iTunes crashes or won't play an MP4tools created file: This is typical of videos with only AC3 audio files. Though streaming these files to an Apple TV will work, the usual fix is to also include a 2-ch. AAC copy of the audio file that Quicktime/iTunes is happier with.
- When played on the Apple TV, the resulting video is out of sync, stutters or won't play: To maximize the speed of processing and optimize picture quality, MP4tools tries use video pass thru whenever possible. One way it does this is to fool the Apple TV into playing movies that our not within its video specifications. Usually these videos will play fine, but sometimes you'll encounter problems. Sometimes setting a different device option, which will change the avc profile level, will resolve the issue. Otherwise you might just have have to reprocess the video with either 1-pass or 2-pass encoding.
- Joined videos are not playing properly: Joining can be hit or miss. Usually it requires a complete re-encode like what quicktime does, but often we can get around that, which is what MP4tools tries to do. Success mostly depends on how the originals were encoded . For example, it seems that handbrake encoded files can give bad results, though I'm not sure why. There are some tweaks that you can try when you don't get good results. Joining just a few files at a time can be successful. Processing the files through MP4tools first (passthru or you might have to re-encode some of the tracks) can also improve results. Also, if the originals are MKV videos, you could try joining those files with something like MKVtools and then re-encoding the joined videos. MKV's tend to be more forgiving than MP4's.