I should probably elaborate on my question for two reasons.
1.) Gain. Gain is fun. Used right, gain can sound awesome. However, gain is also in some ways a dynamic effect, squashing your attack and extending your sustain, so there's less audible difference between your pick attack and everything after that. For lead guitar, that's sometimes a good thing - effortless sustain and smooth attack can lead to a very vocal guitar sound. For a rhythm track, though, you want some of that impact, and a super gainy sound can sometimes turn a fast strummed part into an even wall of mush. This makes it more likely to slip into the background behind other instruments, even if it sounds "cool" on its own.
2.) midrange. An electric guitar is, exaggerating only slightly here, all midrange. Scooping the living fuck out of your mids and cranking your treble and bass may give you this evil "chunk" sound when you're playing alone in your room, but the problem here is what happens when you add in other instruments. Your boosted lows will have to compete with the bass guitar and kick drum, and your boosted highs will have to try to cut their way through the cymbols. In both instances, they'll fail. Meanwhile, with a strong mid cut, the one frequency band which is almost uncontested for the guitar (the mids) will just have nothing left in it.
Combine these two, and an evil, chunky metal rhythm tone can turn to white noise as soon as you add bass and drums. If you have no trouble with leads, and especially if you're playing through a notoriously over-gained amp like a Line6 or a Randall, then based on your "incredible dissapearing rhythm tone" my first instinct would be to check your gain and midrange knobs.
