It's not very clear from your message if this is a problem you always had, or you just found out, or if you are new to GSX, or you are new to FS Labs. I'm asking because we surely haven't changed anything in quite a long while the way GSX detects if engines are running, and nobody reported this before.
Also, is not clear from your message how you are using GSX and the FS Labs together. If you are letting the plane controlling GSX, have you tried to see if GSX detects if the engines are started when using GSX manually, without the airplane controlling it ?
Also, if this issue is happening at the end of the pushback, Abort is not your only choice, if for any reason you need to skip the engine started check from GSX, choose "Stop here and complete pushback procedure", which will end the pushback gracefully, better than the Abort, which might have issues with the FS Labs custom bypass system. Will check this but, for the time being, don't Abort.