It sounds like there’s a problem with the hold shorts.
Or a bug in SU11.
I’m working right now and have a concert to go to right after work. I’ll try to take a look at it tomorrow or Sunday.
Are you using the AIG or FSTL or whatever they are AI packages? (I’m not, so I’m not sure I’ll be able to replicate the issue if so).
Navigraph? I think it has it’s own airport database that may overwrite the taxiway/runway network as well, so loading order would matter there.