I can request for boarding/de-boarding for these two gates, however after the services has been completed they will not go back to their original position
They are not supposed to go back until you go away with pushback. This change is not new: we added in the previous update, 6 months ago, because now that simultaneous services are possible, bringing back the loaders would cause a conflict with a refueler or a catering vehicle, which now can be called at the same time as boarding.
example the baggage handlers, they will just keep on standing and do nothing and when I try to request for pushback it says "waiting for other services to be completed" even though it has been complete.
If it only happens in specific parking spots, it's possible the scenery AFCAD has some problems (orphaned nodes, overlapping nodes, unconnected links, etc.), so GSX couldn't find a proper path for some of the vehicles.
It would be helpful to have a look at the scenery AFCAD, you might send it to me by email.