Since I updated the firmware the transpose sounds robotic

1) As suggested by others, you should use the transpose, rather than pitch shift for the kind of application you're looking for from the effect.
2) Have you got headphone space linked to your outputs? That would explain why the effect doesn't sound so good through your cabinet, but alright through your interface.

You should put a transpose effect to the stomp section, not the effect section.

Then there might be the chance of doing some recordings with everything working perfect and if if stops working with the "faulty" sound?