Perfect, thanks for the tip on partial exports.
I just had a look at a couple of the last segments I added to the sequence. One of them was 1080 x 1920, whereas all the other segments are 1920x1080.
I'm guessing that when you start the export and it looks at all the files, it's seeing this last segment as the rule for the resolution.... maybe?
Solved.... in the time I was typing this post the export test finished and that was it. The last segment res is what governed the cropped output.
I was sure that I tried the "force" option once when exporting but regardless it didn't seem to work like I thought it would.
Next I will add back in the template for the scaling and I should be fine. Then I'll figure out how to use the odd segments step at a time.
Thanks for the input people!