Whats the real difference between .m4v and .mp4, if any?
is it just chapters i heard chapters cant be used in .mp4.
When i do an encode like on the apple tv preset can i just change the .m4v to .mp4 without making it incompatible
From the Handbrake user guide: "In an MP4, you can store MPEG-4 video created by ffmpeg, XviD, or x264. It stores audio in the AAC format. It is also possible to pass through Dolby Digital 5.1 Surround Sound (AC3) audio from a DVD in an MP4 file, although it is a new standard and not widely supported. Perian and VLC can decode it, and the AppleTV can pass it through to a surround sound receiver. MP4 also supports chapters, for which HandBrake uses Apple's chapter format. MP4 also is capable of storing Variable Frame Rate video. Be aware that chapters and AC3 audio can only be seen by QuickTime if you change the file extension from .mp4 to .m4v. HandBrake will do this for you automatically when you enable those features, although this can be disabled in the preferences if you really want .mp4 at the end of the name. The MP4 format can also be optimized for "fast start" progressive downloads over the Web."
So, it's not that mp4 can't have chapters. Rather, it's that quicktime won't see them unless it's named m4v. If you change the extension, the chapters will still be there - quicktime just won't acknowledge them. They'll still play, though.