I have a question Darknailblue.
What other effects are you using when you play distorted?
If you use lots of reverb, delay, or chorus, or combinations of these while distorted, it will muddy up your chords.
I do alot of proggy metal stuff too, and have problems with definition if I use combinations of effects with alot of gain and distortion. I have found that if I back off off those effects, or run dry or with maybe a touch of 'verb, the muddiness tends to go away, at least enough to hear the chords.
Also, if you're playing a seven string thats detuned, the bass strings tend to be powerful and kill the higher notes. I don't play detuned for this reason.
Let me know what you find, as I'm always looking to improve my sound.
Good Luck!