I would check all connections. Starting at the battery & working back. See if there is a large amount of voltage loss after the fuse holder. I would highly suspect a poor ground/lose ground, main 12V supply, Accessory 12V turn on, or signal cables.
Are you using an aftermarket amplifier along with your sub?
What kind of vehicle?? (yr. make & model please)
To me it sounds like a wiring issue of some sort. Without going through the system myself, it is very difficult to diagnose.
