This was a brand new repository, created by first committing the changes from the existing database...
The discrepancy is a single row that exists both in the DB as well as in the repository. Here is the full statement:
INSERT INTO [dbo].[FILE_TYPE] ([FILE_TYPEID], [FILETYPE], [DESCRIPTION], [ICONIMAGE], [VIEWABLE], [EXTENSION]) VALUES (N'x-zip-compressed', 'ZIP Document', NULL, 'Zip.gif', NULL, N'.zip')
This is repeated on both sides of the comparison, but one one side it says "Only in Database" and the other side it says "Only in Source Control"