I am not using a RB1000, but x86 based RouterOS on a PowerRouter 2242. Same issue here. Terminating 600+ PPPoE customers and the queues will fail, disconnecting all users until the unit is reboot. We have tried several versions of RouterOS including 4.9 and the problem persists.
The previous suggestions from Mikrotik staff either do not work, or are not usable in our environment. (We need simple queues to assign specific bandwidth profiles a customer is paying for which is passed from our RADIUS server)
This can happen once a week or a few times a day, it is very random. It does seem to happen more often if we have multi cpu support enabled. We cannot contact Mikrotik support since we purchased our license through a 3rd party. This is becoming very frustrating for us, but even more so for our customers.