Sounds like you're using too low a frequency for the high pass filter dude.
I set mine at no lower than 10Khz. At 10KHz, it doesn't drastically alter the tone, it just removes a bit of the really unnecessary air and fizz from the tone)
You need a little bit of the "air" frequencies of guitars that exist around 7KHz upwards to get a professional vibe to your guitars, but the key is not having too much of these frequencies and of course too little is dangerous too.
While I'm no pro at this, I've got to the stage where I can hear that stuff happening in guitar tones.
Some guitar tones, like End of Heartache by Killswitch Engage and Colors by Between the Buried and Me have just enough air not to sound muffled, but they sound quite smooth and rolled off in the high end compared to say, This Godless Endeavor by Nevermore or Around the Fur by Deftones.
It's just a matter of finding what works for the mix and what suits your ear really.
Personally I prefer the Colors/End of Heartache approach for most stuff, unless it's really aggressive, which is why that extra high end works for This Godless Endeavor, because aesthetically and musically it's just such a dark and aggressive piece of music