Is the navigation path being generated correctly in all these cases and is Fly To still running on the BT? I don’t think a case like this has been encountered before. Do you have multi-threading enabled by any chance?
Without anything in the logs at this point it’s hard to guess what’s going on. If you’re comfortable with debugging I suggest putting a breakpoint inside BTTask_FlyTo.cpp’s TickTask function. It should be easy to tell exactly what’s going on by doing that.
Another approach is to carefully compare your setup with the sample project’s manager class, its pawns and its behavior trees.