Both these issues happen to me on a regular basis (BB running 1.6.2).
I don’t think they are related. When I get the message that the file doesn’t appear to be Gcode, I hit OK and continue on. The file will work just fine if the BB is willing to load it!
The other issue where the BB controller gets stuck trying to load a file ….. that sometimes happens to me when there are NO OTHER Gcode FILES in memory.
To fix it, I load a random Gcode file from some past project that I know uploaded without difficulty. Then I just leave it there in the BB’s memory.
Now when I try loading the problem file again, it loads fine.
I hope this fixes yours too. The BB can be a quirky machine.