Are you using Win7 x64? This is a known issue (SOC-675) on this OS...
The upgrade completed successfully, but you won't be able to use the new version until you restart SSMS. If you restart, and then select Help on the SQL Source Control tab > About, could you verify that your version is v0.4.1.2?
FYI - To reinstall, you can uninstall SQL Source Control from Add/Remove Programs and then download the latest version from the announcement posted at the top of this forum
Thank you for the feedback. This is only an issue on Win7 x64, which we hope to fix at some point. On all other OSs, you are prompted to close SSMS yourself and you can not install until you do so. On Win7 x64, it just tries to close SSMS by itself without warning you.
It may be best on the "Check for Updates" to click the "more information" link. This will bring you to a page with the download link. You can then close SSMS and start the download. I know this is kind of an awkward workaround for now, but at least you can be sure that there won't be any problems with the update.
Thank you so much for reporting this! I hope this information helps.
Stephanie M. Herr
SQL Source Control - Project Manager