Good call, I had a funky fuse before. Looked fine, but gave me all sorts of hell.
Like everybody else said, this is a case probably best addressed by starting over. You've eliminated the amp, you've eliminated the RCA, you say you've eliminated the headunit;
Check the wiring in the enclosure, inspect the tinsels, try different subs, unplug/replug harnesses, make sure no stray strands of wire are shorting anything (which may send your amp to protect for a moment) etc.
Use some good common sense and track the problem down.
probe, analyze, isolate, resolve.