I think that you have covered all the regular bases. If I were you, having eliminated all possibilities I know of, I woudl take it in to a car audio place and have it fixed. Try to avoid using a filter, but you could do that if you have to. Take a look at this web site as they have some nice stuff for specific problems. When I installed my Blaupunkt Powered Sub I discovered that my preamp outputs on my headunit were only 500mv. I bought a nice compact line driver from them to boost that signal to 4v (normal). It was very reasonable and I was surprised at all the products they offer. Anyway, good luck as I am out of ideas (sorry).
http://www.davidnavone.com/