MC 6 has some known issues with long quicktime exports. So, I cannot give you a fix without making you change your workflow a bit unfortunately.
If you’re using MXF media (not AMA) then export a quicktime reference movie. This will be a much faster export and will be 100% quality to your edit. The resulting quicktime can be imported into Sorenson Squeeze (or any other encoding app) to create the proper H264 that you desire.
If aren’t using MXF media (such as AMA files) Then you will need to create a video mix down of your timeline first. To do this, clear your in/out marks on the sequence, and highlight all tracks. Then SPECIAL > Video Mixdown. If you wish you can also do an Audio Mixdown in the same fashion, just SPECIAL > Audio Mixdown.
These mixdowns are full quality MXF versions of your edit. You can then create a new sequence containing only the video/audio mix downs. Doing a quicktime reference movie will work and will be super fast (about 3-5 seconds). You can then, once again, import this quicktime reference movie into any compression software.