The windows were carved into the side of the bus and afterwards I just separated them to relieve texture work. They are exported as separate objects and are completely aligned in Blender
I itsn`t clear to me if you already have seperated windows with a correct allignment in Blender, or if you seperate the windows after you have made sure that the allignment is correct. In the second case maybe the following can help, but I am not sure if this goes up for Blender because I use Zmodeler. Zmodeler sometimes creates very small gaps when seperating objects, you really won`t notice it untill you look very closely at it. For me the solution is always to undo and redo the seperation untill it stays at the correct position, mostly the third time it will be correct.
You can also try to attach the windows to the body and center the cursor again. Then seperate them, center the cursor of the windows and export them to OMSI. If the windows still show the little gap in OMSI try to export the body again after you have centered the cursor of it.