Things are a little unpredictable for me. I just got 93k on Donkey Kong 3, escaped out of the game, my score appeared in second place. I went straight back into the game and had another go, and got 125k...escaped out, expecting to see myself at the top, and nothing...no upload of the second score.
The only thing I can think of is I changed the mapping of the fire button to a different button on my joystick, but surely that wouldn't have caused the score not to upload ? (I did do "change keys (this game)", rather than globally.
Edit, just deleted the hi and cfg files and played again, and this one went up. Not sure what one did it, or if it needed both.