Odd behavior when bouncing tracks. Audio Damage Replicant

Quick question.  I am using Audio Damage's Axon (tone generator) followed by Audio Damage's Replicant (delay and glitch effect) plugin.  Anyway, when I use that in the FX bin it works just fine.  However, when bouncing down tracks, the result is different and not desirable.   My work around was to bounce the Axon track alone and then apply the Replicate to the bounced track. Then I play the Axon track in real time and record the track by physically recording the outputs of my mixer into a new track.  Even if I bounce the axon track with the replicant it comes out wrong.
 
Have any of you experienced issues where a bounced track with an effect is different than when it is playing live?  I suppose my work around is ok but seems less than professional.
 
Any thoughts?
 
Thanks
 
Joe