Due to changes made in the MS/CS requirements since 2004, when the combined degree/certificate program was designed, the courses outlined for that combination are no longer valid. The CS department changed how certain SWE courses were classified, making it impossible to obtain the certificate in SWE in conjunction with the MS/CS degree, without taking at least two additional courses.
The SWE department, on the other hand, has no problem letting CS courses count towards a MS/SWE.
My job is as a software engineer. The largely thoretical aspects of Computer Science do not typically come into play on a daily basis. I'm not writing compilers, I'm not doing anything with artificial intelligence, I'm not designing operating systems or massively parallel computational systems. Computer Science just doesn't apply to my daily life as much as Software Engineering does.
For these reasons, I am strongly considering changing degrees. All the courses I have taken so far should transfer to the new program, allowing me to get a MS/SWE in the same time frame as I would have otherwise gotten an MS/CS.