If it sounds good in the software, but doesn't sound good with the pedal into a cab or PA, then either something is going on with your gain staging into the pedal, or something is wrong with your playback setup, or both.
Are you possibly clipping the input of the Tonex pedal? How do you have the input trim set?
When you're using a PA, are you using a cab sim or IR? What about when you're sending the Tonex into a power amp and cab?
How does the pedal sound being fed into the same playback system (headphones, speakers, whatever) you're using with the software? If input levels are matched between software and pedal, it should sound basically the same as the software.
While it's possible and valid that you may not like Tonex, I think it's great to keep in mind that a lot of people get really good sounds, and that you're getting good sounds in software, so it's most likely an issue like this rather than Tonex itself being bad :)