I just wanted to post an update on this.
I was noticing the same thing recently. Some of my pedals sounded "nasal" thru the clean channel. In order to fix this, you have to switch on the BRIGHT switch, and then back off the TREBLE knob slightly.
It's funny - you can get a great clean tone with the bright off, and the treble cranked pretty high. Or you can use the bright on, with the treble at a normal range. Both of these sound VERY similar when the amp is set clean. But when you run an overdrive pedal into it, you really notice that the treble knob is affecting the high-mids, and the bright switch brings out that upper-high sheen.
Oddly enough, having the bright switch engaged results in a MUCH more natural sound from overdrive pedals.