I submitted this issue to support@mikrotik.com i think 3 times now, and have never heard back from them on the issue.
After running a firmware update, in fact any firmware past 6.42.x causes multiple devices to lock up, and causes the DHCP server to not start, the CPU is at 100% and barely passes any traffic. The logs show unable to start a program. Note: only 4 out of hundreds so far, but it's still devices that should be working well.
The issue at this point is that Sonar cannot connect to these devices because they're a lower firmware version not using the new authentication methods. Which i'm assuming is the root of this problem. I wonder if mikrotik can help us fix these or get them RMAd.