Encoder only exports first 30 seconds of clip?

Hello,

I have been trying for a while now to transcode .MXF files (Shot on a Sony F5) to ProRes 422 so I can use them with premier Pro (Premier crashes every time I import the files in to media browser). However when the footage has been transcoded it only has the first 30 seconds, when the clips are often much longer. The file structures are all correct, and this is not a trial version. Does anyone know how to fix this? I'm operating it on a mac OS X with 16GB RAM.

Thanks in advance!