1) The stock voltage meter is accurate for voltage at the batt, the problem is you need to know voltage at the amp. Buy another volt meter and run it directly to the amp.
2) Im surprised no one asked but whats the HU settings for sub output
3) Do you have an ipod with the RCA adaptor, if so, hook the ipod up to the amp and bypass the headunit and see if the headunit is the problem
4) Check the sub wiring, something could barely be making contact and causing an issue
5) Check all the wiring at the amp and make sure a strand or something isnt branching over to another terminal.