Difficulty getting HF filter to work: maybe PCB layout?
On a subsequent iteration of the board I realized etching the board was unnecessary work for a prototype, and I could just isolate the sections with an abrasive wheel. Once I did this I got reasonable measurements on and off board.

I think it's the "loop" that's formed around the capacitor pads causing the issue:



I'm guessing this was somehow acting as a turn of a transformer and coupling with adjacent sections or the components soldered across them.