AMA, Please Explain...

I just watched the AMA Supersport race at Infineon Raceway (the same place that claimed the racing career of Vincent Haskovec) and I am completely confounded by the race result. According to AMA timing and scoring they gave the race to Josh Hayes even though it was Jamie Hacking who crossed the line on the last completed lap before the red flag came out. Yes, the red flag came out due to the fact that someone crashed bad enough into some obstacle to need the race to stop. Regardless, it was Hayes who grabbed the lead for less than ten seconds, between a couple of turns, when the flag came out. Is this how it works in the AMA rulebook? I've got to get me a copy.