wah pedal and line 6 flextone problems

ok, i just got a line 6 flextone series 60 watt combo, and i also own a morely bad horsie 2 wah, i used teh wah in front of my amp, and in teh fx loop of my amp, but i still got a problem. The problem is that when i press down on the wah, the distortion of my amp sort of mutes and i didnt ever have this problem with my old ibanez 12 watt combo and it would keep the same distortion but make teh wah fluid and stuff. i own a distortion pedal, a boss mega distortion, and i was thinking maybe if used that pedal in my effects loop and set teh line 6 on clean, i could use teh pedals crunch and maybe teh wah wouldnt mute it, but i havent tried it yet for lack of a battery. so if anyone knwos what im talking about just gimme some advice