There's a new version 2.00 of the PLP app to download here: http://xgn.com.au/index.php?topic=758.0
This version only issues a cut track warning if you've gained time by the cut.
How it works: it divides the track up into little sections and keeps the average of your last 6 times through that section. If you've cut the track in a section and you're more than 5% faster than your average as a result, you get a cut track warning.
If there's not enough valid times recorded yet for a section (e.g. at the start of a race or if you keep cutting there), it falls back to the old style cut detection in that section.
For the curious, it logs the cuts in Documents\Assetto Corsa\logs\py_log.txt.