When in Auto Pilot, the cursor moves just like in Auto. This thus assumes you'll hit every note when you should.
If you're on a map with jumps, however, and you hit too early (enough to get 100 in normal play), the cursor won't be on the note, and you'll effectively miss. Similarly, if you hit too late, the cursor has already left the note you intended to hit, causing a miss.
Possible solutions are to ignore the cursor's position or to move the cursor quickly to the next note. The former may not really make sense, but it solves the problem. The latter is plain goofy but makes sense as a solution.
If you're on a map with jumps, however, and you hit too early (enough to get 100 in normal play), the cursor won't be on the note, and you'll effectively miss. Similarly, if you hit too late, the cursor has already left the note you intended to hit, causing a miss.
Possible solutions are to ignore the cursor's position or to move the cursor quickly to the next note. The former may not really make sense, but it solves the problem. The latter is plain goofy but makes sense as a solution.