This sounds like a possible effects loop problem. They can get corroded if you don't use them, and could probably use a good cleaning with Deoxit contact cleaner. Try that first of all...you can also run a plug in and out of each jack several times really fast if you don't have any contact cleaner.
Also, not sure if your amp has any tubes or not, but if it does and the cleaning doesn't work, might want to check that out next. Beyond that would require a tech.
Ampeg Portaflex Club #1