toddrico:

I can send midi CC from an ableton clip envelope and I thought it would be great to automate the state of the patch active/bypass by drawing automation in the clip envelope for the corresponding midi CC. I'm using CC3 for Bypass and CC4 for Active.

Disclaimer:  I'm familiar with Ableton Live (in the past), but I've used Sonar and other DAWs for years now.  First question:  Is there a reason that you need to use two separate CCs for Active and Bypass?  I would go with a single CC message bound to one or the other, or use the 'Toggle between Active & Bypass' setting (my preference).

I'm guessing here. I don't have any knowledge of your system setup, that plug-in, or how you have the envelopes drawn.  But you only need a single CC value to turn a 'switch-type' parameter on & off.  You may have an envelope drawn that is transmitting many 'OFF' values in a series, before it reaches an 'ON' value.  But I would think that would result in many converted CC-to-Program Change messages in a series.  Perhaps too many for the PitchFactor to handle.  Again, only a guess.

My Pitchfactor is on the latest 5.0.0 beta 4 firmware so I could update the pedal with the H9 software.

Try something like this:  If you're using CC#4 for Active, draw an envelope with a sharp, vertical step; up & down.  In effect, a square wave.  When the value for CC#4 goes to 64 through 127, the PF should be Active.  When the CC#4 envelope snaps down to 0 through 63 for a value, the PitchFactor should go into Bypass.

I have V. 5.0.0 [1] loaded here.  It shouldn't be that much different.  You may find that you like the TOG parameter action for working with externally generated envelopes.