Oxford/Bicester to WML does not work
After the first scenario I tried did not work, I tried the OB Oxford to Bicester scenario and had exactly the same problem. Having driven to the fist stop, Oxford Parkway, the doors would not open. I did continue to Bicester and the doors opened fine at the other stations. Tried it second time and same problem. Obviously the scenario fails as it thinks I have not picked up passengers at Oxford Parkway - OK I haven't but not for want of trying. My guess is that Quality Control does not include running the scenarios. Must confess I think the Oxford/Bicester extension to Western mainlines is a complete waste of money - would recommend that anyone not already bought it probably shouldn't.
I think your best bet would be to contact Just Trains support. The product has been out for a long time and I am sure we'd be aware of issues like the ones you state by now. If they were unaddressed it is likely other users would have made their feelings known.
If support can assist they will.
I had the same problem all support said was try moving the train forward a bit I had stopped in the correct place