SSMS suddenly starts generating DEFAULT constraints inlined into the CREATE TABLE statements instead of ALTER TABLE
This 'might' be the problem, although, there does not appear to be a 'solution'.  I was able to reproduce your issue. See this connect item regarding this problem:

https://connect.microsoft.com/SQLServer/Feedback/Details/895113


  The SQL SMO generates for a table with defaults depends on the rowcount of the table. This makes it impossible to programmatically compare the schema.