The problem is with the workflow.
What you should do is the following:
1. rotate odd and even pages with something like Phatch: http://photobatch.stani.be/
, which allows you to process a lot of photos in one step.
2. rename them and put them in a single directory
3. process them with scantailor.
The problem is that when you run the "select content" option in ST, it doesn't put the same frame for all the photos, that's the reason why you get different sizes for odd/even pages. I had the same problem as you and then I rearranged my workflow in the way I'm describing it and it worked.