We may have stumbled upon the problem (even though it should not be the problem). I was using a Regex to find the correct format for the Tax amount as shown in the image below.
This was working in layout studio. However, in FlexiCapture the tax was not found. Upon removing the regex restriction and letting it just find anything Flexicapture would then work. You would think that this means that the capture studio was finding something that does not match the regex. But no, It found '.22' just like it should have.
Still wondering why it does this. I would like to continue to use regex's as it helps not recognize the wrong thing. Any thoughts?