May have answered my own question, there seems to be a silent error in the CMD line Compare. If I try to perform this same compare via the application, I get an error about the SCHEMABINDING on these Views. One of the tables in the VIEW is being altered, and the Compare from the application fails. The CMD line drops the views, changes the table, then recreates them, but doesn't add the full text indexing.
I've been told prior that MSSQL won't allow creation of a schema bound view and adding a full text index in one step, bummer.