There is a bug in the Nintex Form Build number 22.214.171.124:
If you create a rule in order to disable a checkbox, the value of the checkbox will be reset to False in the FormData even though it was True in the Form.
bug reporting checkboxes
Hey there... I had this exact issue the other day.. I just finished installing the latest version that went out yesterday and it has fixed it for me.. This was a pretty big maintenance release.. Check the change log here..
Nintex Forms 2013 - Release Notes
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