I too built the 60 knobs. Haven’t tried to hook it up via the pyramid like you do but I’m guessing the patches will be sent to the 60knobs as sysex. I think pyramid isn’t passing along the sysex…
TRANSMIT SYSEX If OFF, received sysex messages are ignored. If Midi A (or Midi B, or Midi A+B), received sysex messages transmitted to MidiA (or Midi B, or Midi A+B).
When sending sysex you generally want a direct connection with a standard MIDI cable. USB MIDI is known to not work well for sysex in quite a lot of gear. In other words, you probably need a decent USB MIDI interface. (M-Audio ones work fine, no need to spend a lot).