this doesn't sound installation related (wiring or placement), since a bad left channel would stay bad if it was ... this sounds like an equipment issue (the HU or whatever you are using to do the fading). we know nothing about your system so there really is nothing that can be definitively figured out. At this point I would say HU but it could be the amp or something weird like voltage

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I don't know what your problem is, but I'll bet it's hard to pronounce.