[mahipal]

Note that my answer will be hugely biased, but then again so will everyone else's. ;)

Nonetheless, I'd say to go for the MSCS (or similar). You're looking for the networking potential of going back to school, and you want to start a start-up. In a technical master's program, you'll be around exactly the sort of people you need to meet for this to happen. In an MBA program, you'd network with a bunch of other business guys, many of whom wouldn't be interested in start-ups at all.

You'll obviously also gain a lot of truly valuable technical skills. You might not be able to single-handedly carry the technical side of a start-up by the end, but you'll definitely be able to make meaningful contributions and decisions about the technology. This helps your future partners as well, since they know you can contribute to the tech while working the business side.

If you're worried about missing out on the education side of the MBA, don't be. I think you could get a better version of an MBA education by just buying a pile of books [1] and starting a company. You'll learn everything you need about business along the way. And, as for the networking part of an MBA, you'll get way more interesting conversations out of "I'm running a start-up" vs. "I'm working on my business degree."

[1] Possibly a topic for another thread, but here's an example of such a reading list: http://personalmba.com/best-business-books/