If you're using TimeFactor in a parallel effects loop you might want to turn KILLDRY ON. This is located in System Mode under the BYPASS menu. KILLDRY lets only the wet signal through to TimeFactor's outputs, and mutes the signal when TimeFactor is in Bypass. This is good for a parallel effects loop because when in Bypass you don't want to mix your dry tone with dry sound coming out of TimeFactor. Try it and see if it fixes your issue.
Alan
