IIRC from when I used one, i didn't think that was even possible. The pedalsynth is as separate effect type to the bass guitar triggered synths in the same PRE-AMP module i.e. they can't be used at the same time.
Only thing I can think of is you have some other effects engaged in a different effect block engaged to, like a strong filter/phaser/flanger etc that is effecting both signals. The manual states:
"The pedal synth sound is processed by the effects after the PRE-AMP module, and the bass sound is processed by the effects other than the PRE-AMP module. For information on the effect link sequence, see page 63."
Attitude II SFG; RBX-JM2; Att Std; Thumb 5 BO; Corvette Std fretless; LMII; MB 121H; Nova Dynamics; EBS Billy Sheehan; BEQ-50(x2); Mooer ABY; LS2; BSW; MS-60B; PT Jnr.