I thought if it worked in TS2010 it would work in TS12
Since I use BBL (Sounder) for commuter rail, I need low level platforms and use AJS invisible stations everywhere, adjusting platform splines as needed and then adjusting invisible station passenger height and shape as needed. Most work fine.
I have noticed that (in TS2010) one AJS invisible station resets platform height and passenger shape if you move it after getting it set up. Maybe it is more of an issue in TS12. This was not an issue in TC1&2.
Try to get the station exactly in the precise place and then leave it alone, then set up the passenger height and shape. Maybe that will solve the problem.