I’m not sure which Module you are specifically referring to, but I had print configuration issues last week when I was setting up forms to print in the T3 Module. This was under Options–>T3–Print–2018. It seems, once I created my custom configuration, as well as name the print sets, the configuration would not save the settings if I hit “Apply” then “OK” to leave that screen. I found that I needed to hit “OK” without hitting the “Apply” button in order for TaxCycle to save my print settings.
Perhaps you can try that.
This happened to me a few years back, so I remembered how to work around it.