If they're getting stinky, definitely root rot.

But from your last post, sounds like you have the usual culprits at bay. In fact, you might be over doing the peroxide, which can damage the roots, although I don't know if it would brown them.

Nutrient burn can cause brown roots. If you've let the TDS get a little high at times, that could be how your roots got their tan.

Also, if it's root rot, the plants should start to show some problems on the top side as well.