I had this problem on several flights now (also with version 3.0.1):
I notice that I'm not handed off to the next Center when I should be. I check by "request direct" and find that PF3 is way behind me regarding the actual waypoint. Fortunately I can request a direct to my actual waypoint and everything is fine again. But if I don't do that I won't receive descend and approach instructions later on, because PF3 still waits for me to reach that long gone waypoint.
And despite having the airway deviation distance set to 10, PF3 did not warn me. Only when I ask for vectors ATC tells me something like I'm 80 miles off the airway.
I did not actually miss these waypoints because the route was flown by the aersoft airbus autopilot without issues.
I checked the same flightplan again with the "warning if waypoints are too close" checked and found that there were warnings and these actually were the waypoints PF3 obviously had problems with.
So this problem still seems to persist.