Here's what I tried out today after a suggestion from (moderator) Morgan. I changed out R2 for a potentiometer, which if you didn't already know, is pretty much a variable resistor...Check out this thread:
viewtopic.php?f=23&t=2856&hilit=potentiometer+for+resistor...and I followed baj2k method (2nd post on thread) to mess around and measure different resistances and the effect on the sound.
I suggest trying this with a 500k pot (or maybe a 250k) to find what works best for your setup...for me, I found that with the guitar and amp I was using, past 185k Ohms you lose the Filter effect, but prior to that (the range may vary depending on your setup) there is a noticeable level drop when I click the pedal on, and then click it off.
I am not sure how this will affect the exact issue you are having, but its something to look into. Using a multi-meter, once you figure out what value resistance you need you can get the appropriate resistors to do so.
Or another suggestion is perhaps a mini-trim pot so you can adjust it as needed as a resistor swap would be a bit more permanent, but not adjustable.
Try this out, and let us know if it helps fix your issue any, if not, there may be another way to take care of the issue...