I do get quad pain if my saddle's too low, but that's in a very specific place and I've learned to recognize it--outside of the leg, somewhere in the middle--and it goes away as soon as I get off and stretch. Quad pain from the wrong gear is very different and involves pretty much all of the muscles that make up the quadriceps. And it doesn't go away.

OP, do you use clipless pedals or straps/toe cages? Those can help give your quads a bit of a break. It's hard to pedal "properly" with just platforms (especially if they're the horrible slippery plastic kind) because you can't pull up, but you can utilize a motion similar to scraping mud off the bottom of your shoes to complete as much of the circle as you can.