HitFilm exporting/importing problems

I've been experiencing a number of problems with my HitFilm Express program lately. I've been working on videos from a 5D mk II camera, and the program does not seem to handle them very well ('not very well' meaning not at all).
When I finished editing and exported my video, the exported version had a series of faults in it. Several shots are pixelated, and often choppy (sometimes slowing down to 1-2 fps), while the next few shots would be fine. When I retried the export, the same would happen to other shots that were fine in the first one, so the issue is not with the footage itself (I checked all the shots seperately in VLC media player).
This means that the video is basically unusable and unenjoyable... Of course I wouldn't run to the forum here before doing my research. My computer is quite capable of running hitfilm, even though it is not a super-fast editing station, the specifications are more than adequate. So the second thing that people recommended when experiencing similar problems was converting the H.264 files into DNxHD, which I did using MPEG Streamclip. That's when things just got worse...
HitFilm refused to import these files, displaying only blank white shots for the clips on the timeline, so I couldn't even start editing the DNxHD versions.
Does anyone know how to fix these issues? I have a deadline for this project and I'm getting quite frustrated by all these problems. Even though I'm using only the Express version, it was way too much money to pay for a non-working program (yes, I bought it before they gave it away for free).