So, to sum up what we know:
1: As posted by David, Alex doesn't do things lightly, is usually very open about why changes were made, etc.
2: Several people have asked why. We haven't gotten an answer.
Conclusion: Whatever caused the name change, it's something where giving us the reason why is worse than allowing rampant speculation and conspiracy theories.
Conspiracy Theory: Therefore, the name change is obviously due to some sort of legal shenanigans. It can't be a simple cease-and-desist order, since he could tell us about that. Therefore, the name change & resulting silence must be related to some form of Non-Disclosure Agreement. Therefore, obviously, Valve is trying to buy Fractal Softworks, but required the name to be changed so as to not conflict with their own super-secret project, coincidentally also named Starfarer.
Footnote: The above is a deliberately ludicrous conspiracy theory, and should be taken for comic value, rather than as a serious attempt to explain the name change.