Huh.
Well, if you're getting effected signal out (you're sure of that, now--usually the issues go the other way--bypass, but no effect), I think the only place it could be is the bottom half of your 3PDT.
Look at your solder joints in the little loop there in row 3, going from column 1 over to 3. Might as well throw in a continuity test with a multimeter between those pins, and between those pins and the ones immediately above in row 2. If your multimeter doesn't beep, that's your issue.