I just ran into the 100% cpu issue. How it happened:
* Was logged into RB1100 w/ 5.1 via SSH.
* Was going to /ip neighbor discovery to check settings. In the middle of typing the command the SSH session became unresponsive.
* SSH'd in via another console, it authenticated immediately but the console took forever to display the MOTD (mikrotik logo in text). Never received an actual prompt
* Logged in via winbox, everything working fine, it shows 100% cpu. Even launching a terminal from within Winbox had the same issue- took forever to display MOTD, never gets to an actual shell.
I left it this way for about an hour, it never recovered. Rebooted it. Issue has not occured again yet. I will remain logged in via ssh to see if it reproduces. The device in question is barely doing any traffic and has a single IPSec tunnel:
Is there any way to manually kill connected users/shells? This may have cleared up the problem.