This is going to corrupt your route and the rest of your database. You'll end up running an EDBR at best, or losing everything at worst. At this point, I would run a DBR because not doing so will make matters worse. If Trainz is busy while shutting down, it's closing the open database handles and shutting down gracefully. The process is more noticeable with full hard drives as Windows is swapping data around to make space and also on regular hard disks especially if they are highly fragmented.
As stagecoach says, ATLS crossings use an invisible locomotive to open and control the crossings. If the gates aren't resetting, it means that there's something incorrect with the setup, or as I've experienced, I've not completely exited the circuit. If you don't exit the close circuit trigger, then this will cause the crossing to remain active causing the gates not to open.
The alternative is to use the very versatile TRC crossings. They are a bit easier in some respects to the setup and they have some features such as stopping and starting within the crossing zone with gates going up to allow traffic to pass over the crossing.