*sorry if I’m telling you stuff you already know and/or misunderstanding the issue*
I never have any problems, altho I don’t use any of the stuff you’re talking about.
These days I’ve mostly used their in app course creator, which makes it dead easy, tho I can understand wanting to use a bigger screen for that. In the past I’ve used website bikehike to create a course, saved it and transferred via usb into BCNav/data folder, then from ‘import tracks and waypoints’, overlayed it. In recent BCN updates it looks like you can now import/overlay direct from the phone’s download folder as well. Try creating a short course in bikehike, saving it as a gpx, put it in the phone (download or BCNav/data), see if BCN can find that (from import tracks and waypoints). if it can, then you know the issue is with your current method of creating a course. Also worth looking at justgoride as a site for creating a course (not used it yet myself but my bro in law swears by it).