Seems that Git for Windows was released a few weeks ago, replacing msysgit. There were a couple problems using git-annex with that package of git, which I fixed on Thursday. The next release of git-annex won't work with msysgit any longer though; only with Git for Windows.
On Friday, I improved the Windows package further, making it work even when git is not added to the system PATH. In such an installation, git-annex will now work inside the "git bash" window, and I even got the webapp starting from the menu working without git in PATH.
In other dependency fun, the daily builds for Linux got broken due to a glibc bug in Debian unstable/testing, which makes the bundled curl and ssh segfault. With some difficulty I tracked that down, and it turns out the bug has been fixed upstream for quite a while. The daily builds are now using the fixed glibc 2.21.
Today, got back to making useful improvements, rather than chasing
dependencies. Improved the bash completion for remotes and backends,
made annex.hardlink be used more, and made special remotes that are
configured with autoenable=true get automatically enabled by git annex init.