My wife loves broccoli cheddar soup... she has been trying to master it for a few years and recently got back on the kick (maybe something to do with pregnancy)

The recipe she is trying involves a crock-pot overnight... woke up the wonderfully pungent smell of broccoli. What causes this? I can microwave it, use it in stir-fry type dishes etc without any real stink, but for some reason when she put it in this soup it was horribly pungent. My whole house smells like sour-kraut now... I can't stand that smell...

mmmmm sauerkraut

Sauerkraut smells good.... the broccoli smell you speak of smells like dog shit.  It has to be caused by a chemical reaction of one of the active ingredients in the plant because I know exactly what smell you speak of.
I hate my broccoli cooked I much prefer it raw.