AME Thumbnail Freezes, but keeps "encoding"

Hey everybody, I'll try to be as detailed as possible. If you need any more info, ask away! This is starting to get frustrating.
I'm editing a project shot on Red Epic using the RAW .R3D 5K files. In my initial editing, I changed both the scaling as well as the speed/duration on some of the shots. I then sent the project off to the colorist who used DaVinci Resolve to color correct the footage. He then exported the individual clips as .MOV using the GoPro Cineform codec and gave them back to me.
I then took those clips and overlayed them to match the original footage. Since DaVince reset the scaling and speed/duration changes, I had to redo these.
So at the moment I'm trying to export an H.264 file at 720p for the sound editor to use as reference for mixing, but everytime I try to encode it with AME it keeps getting stuck, so to speak, around the first clip with a speed/duration change. This always happens around 27 minutes into encoding.
Basically what happens is the encoding bar and the thumbnail freeze, but the elapsed time keeps counting and the time remaining keeps going up and up. If I let it sit for hours it won't do anything.
Sometimes it'll get stuck just before the adjusted clip, sometimes it'll get stuck during it, and sometimes it'll get stuck right after it; but always in that area.
I look at Activity Monitor (using a Mac with new OS X Mavericks) and the Adobe QT32 Server is always in red text and "not responding"
If I try to export straight from Premiere Pro, I get an "Error Compiling Movie" with no further explanaition.
I'm using AME 6.0.2 and when I open the updater, there are no updates for it.
I have successfully exported this before in the H.264 codec, but I'm sure this was BEFORE I updated to OS X Mavericks and don't know if that's the culprit.
Any ideas?

I'd need to transfer everything onto the local drive, which could take some time, but I should be able to. The external drive (G-Raid, Raid 0, 7200 RPM) is connected via Firewire 800 to my iMac. I also have everything backed up on a LaCie drive, but it wouldn't be very optimal to work off of it.
Here is some more information based on the things I did/tried today. Hopefully I can explain this clearly...
To begin, I essentially have 3 sequence:
Sequence 1 contains the RAW uncolored .R3D files, which have been edited.
Sequence 2 contains the .mov colored files matching the edits on Sequence 1
Sequence 3 contains a counting leader, sequence 2 (on the timeline), then the closing credits.
The sequence I'm trying to export is sequence 3. If I tried to export it through PPro, I got an "Error Compiling Movie" message with no explaination. If I tried to use AME, it does what I previously described. If I tried to export sequence 2, I had the same results in both PPro and AME. If I tried to export sequence 1, it would complete the export but change the .mp4 to an unplayable .m4v for some reason.
I felt like this problem was stemming from PPro, so I decided to uninstall/reinstall it. After the reinstall, I tried sequence 3 again in AME with the same results. I then rendered preview files of all the 5K clips on sequence 2. After I did this, I successfully exported sequence 2 as an H.264 file with all the settings I was trying. Finally!
Now on sequence 3 I have sequence 2 placed on the timeline, mainly for ease and organization. Even though I rendered preview files of all the clips in sequence 2, it still has a red bar above sequence 2 on the sequence 3 timeline indicating there are no preview files. So I decided to do the same thing and render the preview files. However, this time when I tried I got the "Error Compiling Movie" error again.
The thing that's most frustrating is that I've rendered out this sequence 3 multiple times with no issue. Whenever the sound guy sends me a new audio file I like to plug it in and export it so I can watch it without my computer trying to play catch up. He needs a version of the short film with credits, which is what I'm trying to export for him, but all these problems started.
Sorry. This is an AME board and I'm crossing into PPro territory now.

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