On closer inspection... The fliptop preamps work fine, it's noticeable on the other amp mods I've tried (the distortion of the tube amps really brings it out) and when I use a distortion pedal mod into the fliptop it also happens. So it seems to be the distortions that don't like the 5 string.
I plugged my darkglass into the pod, through the fliptop and it's perfect.