Ok I may be reading this wrong OP, but are you saying...
1) You plugged into the effects return and got proper volume, but when you plug into the normal input that's when you have issues
or
2) You put a cable connecting the effects send and return together, then the amp sounded fine. But if you just plug straight into the normal input without the effects loop jumpered, the volume is too low?
It's sounding like #1 at first blush for me, which just makes me think it could be any number of things in the preamp section. If you're going into the Effects Return ("Power Amp In" I think they call it?), I don't think you'll get anything but the Boost knob and Tweeter/Woofer volume knobs in your signal chain before hitting the power amp section of the amp. It should be bypassing the Pad, Input volume, shaping, and EQ sections.
Either way, I'd take it in for repair. A workhorse amp like that exhibiting issues is kind of concerning, but nothing lasts forever....well, except the Earth and Sky, I think?