There's something about that master file. After re-encoding, there is no resolution change, jumping or freezing on the export of Sequence 1. There are no fonts in that sequence.
Normally, when individual sequences are built, as yours were with fonts, those sequences are then assembled (embedded) into a new sequence and that is the sequence used for the final export. This doesn't seem to be the case with this project, and the sequences themselves also appear to have problems.