We have seen this issue on both our Dev and Prod farms where trying to use the "Check list item permissions" condition will not stay saved.
In other words, we create a Run If action, a Set a condition action, whatever. Then we set the action to run as the workflow owner, and try to use the "Check list item permissions" condition to see if the person in the item's Modified By column has Full Control permissions.
All seems to go well, we save our configuration. Then after closing the action, and re-opening it the previous settings we made are gone. When we try to publish the workflow, Nintex complains about that we didn't configure that action.
Any idea why this is happening?