It would probably help if you shared specs of your machine.
Also, and this one is REALLY important, what exact version of AE are you using (down to the decimal point)?
Where are these files stored? What's the data rate of the r3d file and what is the data rate of the QuickTime you're creating? Also, what codec did you create it in?
Ah, ok. I have a mid-2012 Mac Pro, with a 2 x 2.66 GHz 6-Core Intel Xeon processor, 24 GB RAM, an NVIDIA Quadro K5000 4096 MB graphics card, running OS 10.8.5.
My version of AE is CC 22.214.171.124, and the files are on a SAN I'm connected to through FibreJet. (just tested 370 MB/s write 466 MB/s read)
Data rates: r3d: not totally sure, but the file is 1.73 GB and is 26 seconds long, so... 66.5 MB/s? Quicktime file (ProRes 4444): 1813 mb/s (according to quicktime pro 7)
Has anyone else had this problem? Any ideas if it's fixable?