My 2000 1.8 turbo beetle stalls/shuts off when I brake from 2nd gear. Only seems to happen when I step on the brake when coming to a stop from 2nd gear or roughly 20 mph. Has anybody seen this before? the car will start right back up. If I take it out of gear (manual trans) before applying the brakes it doesn't shut off. check engine light doesn't come on.

Sounds like a malfuctioning brake light switch. Have you done the recall on the brake light switch?