Ahhh. It only happens on the RR model for me!

On checking in the C:\Users\<username>\AppData\Roaming\Virtuali\Airplanes\CS_B757-200-III_RB535C, there is a gsx.cfg file there. In fact, the CS_B757-200-III_RB535C is the only aircraft listed, even though I have tried different RR versions. If I use a different RR version, the alignment of the stairs is even worse. :(

Anyway. To fix this problem, you're going to have to do the alignment yourself, unless someone has already done that, and is willing to share their gsx.cfg files.