Well first, there is no distortion channel.
The distort works by increasing the gain of the second FET in the preamplifier. With higher gain, this stage is easily overdriven. With the exception of higher gain, the signal path through the amp is the same with or without distort.
If you are getting crackly noises with the distort functioning, my first suspect would be the footswitch, cable, or footswitch connection to the amp. The footswitch grounds a connection which allows a source bypass capacitor to affect the second stage.
I would first eliminate the footswitch by connecting an RCA plug directly to the footswitch jack and shorting the ends together.
If this removes the crackle, then the footswitch or cable is the likely suspect. If the crackle remains, then I would look closely at the amp's footswitch RCA jack (crud or loose "tip") and it's wire connection to the circuit board.
The crackle could be coming from a dirty distort control, so I would make sure I gave it a good cleaning as well.