I haven't seen anyone with a similar situation so far, but I have an SK-450 with an APM 2.5, and I'm having problems switching from "takeoff" to the rest of a mission and from the last waypoint to "land". More specifically, it will takeoff and loiter at the takeoff waypoint, but will not transition to the next waypoint. The same happens with landing, where it will fly to the last waypoint and (loosely) loiter over the landing point, but will not land. In addition to this, jump refuses to work. Triggering takeoff and landing separately by setting the mode on my tablet works perfectly fine, it just seems that the mission progression won't switch.
I have had this problem on 3.0.1 and 3.1.2. I reflashed my eeprom, updated to 3.1.2, and reloaded my config, and I still have the same problem. I've attached logs of multiple auto missions, sorry for the length of the logs, I was on my tablet. Also, there are some points at which I'm using follow me, which is great for getting exercise :) I also have my config and testing mission attached. Any help is appreciated, thanks in advance!