So I turned my system on this morning driving to campus and as soon they came on the started making a repeated thumping noise. The bass comes out but it just makes short quick thuds over and over. I've never really heard anything like it so I'm not quite sure what to look for.

 

check all your connections, could be something loose but it could also be your amp starting to go bad....

 

Had a similiar problem with my Total 4-Channel, it is the amp, was starting to go/now is bad.