Hi JBurd77, i have the same issue with only one clean sound that i am using (profile name which i cant remember of the top of my head right now) but it only kicks in when i play harder than usual its almost like an explosive sound that kicks in and out quickly above the actual profile sound and its really annoying as it doesnt happen all the time but i do love that clean profile as its not your typical crystalline and has definite body type of sound with a little sustain which most clean profiles lose.
ON another note are you happy with the FR212 using the GT1000Fx amp?
i have exactly the same amp as you and am considering getting a pair of those FR212 speakers (4ohms right/?) to have a stereo type effect setup Left and Right but there doesn't seem to be any indepdendant user reviews of the Matrix GT amps with the FR212 speakers out there nor see many guys running out to get them. So this is a little worrying.
Are you happy with the sound coming from the Matrix FR212 speakers? Have you used the KPA and amp with anything else to be able to compare?
Cheers buddy.
Gerry