I think it is because if the column is True/Yes then it equals 1 and has a value.
But False/No is empty so it can't be compared.
If you look at the outputs of a Get Items for the Yes/No column, the items that are No don't even have a column output.
Boolean are always kind of difficult because they change depending on the system that is reading it. Even within Microsoft it is stored differently between Sharepoint/Excel/Access/SQL Server.
Anyways, got it figured out now, and I will probably forget next time I'm using boolean and then have to look up what I'm supposed to do.