Also it can make a difference where you fret the notes. Further up the neck is preferred, as the harmonic content / overtones make it easier for pedals to track them - certainly true of octave pedals, so might be worth a punt with the SYB3.
For example, instead of playing 'C' at 3rd fret on the 'A' string try repositioning this note at 8th fret "E" string and see if that makes a difference.
Also, have you tried running into the pedal before the amp instead of the FX loop?