Freezes when exporting .mov files in CS4 / Adobe Media Encoder

For the past 7 hours now I have been trying every internet remedy for the following problem, and was wondering if any of you nice people could help:
I just came back from a ski trip, and wanted to make an edit featuring my fiends. I recorded large parts of the trip on my new iPhone, both in 720p 120fps (120.15fps, h.264 1280*720) and the normal 1080p 30fps. iPhone files are in the .mov format. I also recorded some parts on a GoPro hero hd2 camera at both 720p 60fps and 1080p 30fps. GoPro files are in the MP4 format, and i've never had a probvlem with them.
Now all imports fine into premiere pro, and although I had a few problems with freezing while editing initially, this was quickly solved by terminating all unused (non-adobe) processes in task manager.
So I spent a good 4 hours making a 2.5 minute edit of our day, and wanted to export it.
So I selected the sequence, and went file>export>media, selected all of the preferences i wanted for exporting, and sent it to the Adobe media encoder.
The media encoder loads the files for a few seconds, and then starts the encoding process. And promptly freezes. It freezes at around 10-20 seconds (depending on export preferences) after starting to encode, and never restarts. i can then pause the encode, but cancelling it crashes adobe media encoder and subsequently also crashes Premiere Pro.
I may be mistaken here, but I have a strong suspicion that It is quicktime that is causing all this.
So I tried the following:
- reinstalling, downgrading, updating, etc. Quicktime
- renaming file extensions from .mov to .mp4
- all sorts of export preferences, from image sequences to dvd to blueray and dv. (Image sequences, interestingly, occasionally export to about half a minute into the video(also depending on preferences), then freeze)
- crossing my fingers
- checking for gaps in video, found none
- updating premiere pro and media encoder
- throwing my mouse at the wall in frustration
- making a new project with different settings and copying in the sequence
- disabling "Include source xmp metadata"
- making a new user account and trying it there
Is there anything else I can try?
Could I copy the project itself into a different program (e.g. iMovie or Windows Movie Maker) and export from there?
Is there an alternative to Adobe media encoder?
Need more information?
Thanks for the help!
Specs:
Premiere version: 4.2.1
Encoder version: 4.2.0.006
Comp specs:
16Gb ram
quad core i5
256 Gb solid state (system, program files are here)
2TB HDD (video files, scratch disk are here)
Nvidia gtx 660 graphics
Windows 64 bit
1 monitor

I bought quicktime pro today to try this, but to no avail. it just freezes up again during export.
I tried some other fixes on that page, like renaming files to .mpg extension, which worked once during an export of a test sequence (although everything was shifted and it cut off the export at the gopro footage).
Is there any way I can export this project to another program to export it from there perhaps?
Thanks for the help!

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