Maybe it has something to do with bridges...? I have a bridge for every port on e.g. RB100U. Flash/HDD aren't doing anything when 100% cpu occurs. You only need to send some data through the router and it's on 100%. Didn't see this in RoS v5.18 and below.
I have seen it on 5.16 also.
You may be on to something with the bridges idea though. I have noticed it ONLY happens when the device is MIPS-BE and has a bridge carrying traffic on it, and is usually triggered by The Dude.
e.g. MPLS transit routers, even mips-be ones NEVER have an issue, however the same hardware with the same firmware running a VPLS tunnel BRIDGED to a lan interface will have the 100% cpu issue.