Same story here. I recently installed the RT-AC5300 router. Installed app on phone and one of the first things the app asked me to do was upgrade the firmware of the router to 81625 (3.0.0.4.384_81625). Within a couple days, high CPU on both cores. I SSH into the router and run 'top' to see what's consuming the usage, [mtdblock3] is alternating cores and consuming about 40%. The next largest usage is /sbin/preinit (~4.5%). CPU usage is 58.% SYS, 19.7% IO (3.8% user, 12.3% idle, 2.9% sirq). Interestingly, also did a 'df -h' and saw that 100% of the root file system '/' is used. (all other file systems are 5% or less).
I tried a full "factory reset" which forced me to set it all up from scratch again (I did not use a saved config file). Good at first, but after a couple days, back to same high CPU usage
There are no USB thumb drives plugged into my router. Running in default Wireless Router mode. Running adaptive QOS, AiProtection is ON (Malicious, IPS, Infected device), Apps Analysis and Web history are OFF, Traffic Analyzer is ON, No Cloud apps in use (I have no USB plugged in), DDNS is active using a Lets Encrypt certificate, . Wifi is running with SmartConnect active, all channel selections in 'Auto'. A single Guest network on 5Ghz-1, DHCP server active but no manual assignments. WAN side is to a cable modem (DHCP), no dual-wan, no port triggers. NAT active, UPnP is active. Neither Alexa nor IFTT are linked. No IPv6. No VPN. Web access is enabled so I can use the app remotely.
I'm a skilled linux user of 20 yrs, but missing some of the usual tools I use to dig into the filesystem and see which processes are trying to read/write to file systems or devices. The base OS in this one is slimmed down so I haven't figured out where the services directory is so I can stop/start/restart some processes to see if any specific one is responsible.