Well I discovered what was casuing my problem…not sure what else is in your chain but maybe it will help you.

I am using a Radial Switchbone to drive a stereo rig.  The Switchbone has a knob to reverse polarity on the signal. (something to do with putting the amps out of phase as an option for a less focused, more spread out sound).

That was the cause of the trouble.  Anytime I had polarity reversed, the signal dropped from the Modfactor on Flanger/Rotary settings to almost no output.  Instantly came back when the polarity switch was set back to normal.

I don't know if that's a defect, something broken, or working as intended….but it least its diagnosed and I can avoid it. 

Maybe something in your chain is effecting polarity and causing the same effect for you.