I set my amp that way to get the power tubes to distort slightly, not for clean volume. Its actually quieter to do that on my amp. Whenever I do that the pickup noise is gone, for example:
OD channel
Gain 12 o clock
master 12 o clock
The pickup noise is very present
OD channel
Gain on 7 o clock (very low)
Master dimed
Slightly more noise from the amp, but no noise from the pickups on my bass.
But when I run it like this, my mute button doesnt mute the signal all the way anymore.
Thats what leads me to believe the problem lies in the preamp section of my amp.
And the bass does not make this weird pickup noise thing with any other amps you've tried?
It may seem like the higher gain (input volume setting) might be injecting more noise from a noisy bass into the amp, but then it would do it with other amps too.
B-string and others would know better than me, but it wouldn't hurt to look for a bad ground/broken board trace at the input of the amp?