I wound up calling Lacerte about this and was provided a way to override that diagnostic:
e-File>e-File Support Tools>Disable e-File Error <or>
e-File>e-File Support Tools>Clear Return>Return
The representative said to use the first one list initially, and if that doesn't work, move on to the second.
I don't like having to utilize overrides as I feel our software vendor should be taking care of items like this, but it worked on the few we were having issues.