While I understand you're using low level read_handler trends and such to track table scans, so you can't exempt queries there, I don't understand the rationale for having table scans always flagged as A Bad Thing when you go into the Rating/Explain pane. It's well-known that MySQL will choose a table scan in some cases, and it actually can be faster than using indexes. I think there should be, perhaps, an embedded /* */ SQL comment that can override Jet Profiler's rating, so that it doesn't continually flag false positives.