It's absolutely FCPX. I'm not even sure why I posted this in the Compressor forums. There are so many bugs with Apple's software my head is spinning. Now I can't open Aperture because I did a fresh re-install of FCPX. And it turns out, I'd have to reinstall Mavericks every time I do a fresh reinstall of FCPX just to get Aperture to work:
https://discussions.apple.com/thread/4475322?tstart=0
I have four systems... and it's incredibly frustrating when things are working perfectly with one version of a program than all of a sudden they stop working correctly adding additional steps, troubleshooting, reinstallations, more troubleshooting, etc. etc. IE- more time. Instead of editing at any point today, I've been troubleshooting FCPX and Aperture all day long just trying to get the programs to work properly.
My head is about to explode and an iMac about to go through a window.
All my frustrations aside... since my last post I've trashed preferences and reinstalled FCPX, again. I then rebuilt the entire timeline of the project in question into a fresh timeline. This has to be done by copying and pasting bits and pieces at a time. Yea, after the last update, you can't copy and paste an entire timeline into another project or timeline without everything going haywire. Imagine a failed transport in Star Trek... instead of a human being coming out on the other end, there's a mass of jumbled hands, feet and eyeballs in a mushy clump on the ground. That's what happens when you try to copy and paste an entire project into a new timeline on my end, on any of my four machines after any amount of trashing of preference or reinstalling pro apps or OSX.
Back on track, after rebuilding my project piece by piece, manually placing new chapter markers througout, I took your suggestion of adding in and out points. I've never done that before so I hope I did it right. I hit "i" at the very beginning of the video (00:00:00:00) and "o" at the very end (02:00:37:13). The video is 2 hours, 37 seconds long. Not sure if that will solve the problem, but I'll report back after the export process (to m4v 1080p for Apple Devices).
I've only ever exported to a master file (prores) once. My videos are so long that the resulting video file is absolutely huge. It takes and awfully long time as well. I did a lot of tests with FCPX and have found that an m4v file exported at 1080p for Apple Devices looks just like a master prores file when played back. When burned to disk, they also look exactly the same. So I've never seen the need to export master files to prores when I can simply export to 1080p m4v files that look identical, take a ton less time to create and at a fraction of the size of a prores. An added benefit is I send all of my clients the 'master' m4v files anyway. Perhaps the only downside to m4v is compressor won't recognize the chapter markers for some reason. So when I have to make DVD files, I have to create the chapter list in text edit for import. But that's yet another bug that I'm really not too worried about.
I appreciate your assistance, Russ. Your advice is usually always helpful. Hopefully setting the in and out points will solve this issue on my end. And if I'm doing that wrong (setting the in/out points), please let me know. Sorry for venting, and thanks for listening! I just wish Apple would pay attention to these discussion boards. I've tried reporting the problems but they never get fixed with fresh updates.