Sounds like there could be a problem with the input jack itself or a problem with a sound processing component if you are receiving a crackling sound when changing presets. If you made sure to try different guitars and different cables, then it could possibly be the input jack creating the crackling. As you mention though the sound is triggered by a preset change, which is controlled by the main circuit board. To correct a problem like this, a Line 6 service center would need to see if they can repair or replace the part for you. You can locate a Line 6 Service Center in your area at the link below:
This is one our very first amps, so keep in mind parts could be hard to come by for this amp. Give a call to service center and see if they can assess the amp to find the culprit.