Confused by different results on breadboard vs pcb testing (audio/filter values)

This has already been explained to you, but I will repeat for emphasis.

If you insist on prototyping by ear with an analog circuit, cease and desist with the solderless breadboard, especially if you do not have a decent fluke meter ($200) with accurate capacitance readings.

In a solderless breadboard every common bus are plates in parallel, especially the ground/power busses which are long plates in parallel.

See below:

Plates in parallel is the definition of a capacitor.

Design a prototyping board with socket terminals (see harwin/mill max) Swap to your hearts content.

See here for Socket Terminals

Analog circuits is an art form and right now you're being a masochist, your circuits will never be repeatable.