First, turn off compression:
git config --global core.compression 0
Next, let's do a partial clone to truncate the amount of info coming down:
git clone --depth 1 <repo_URI>
When that works, go into the new directory and retrieve the rest of the clone:
git fetch --unshallow
or, alternately,
git fetch --depth=2147483647
Now, do a regular pull:
git pull --all
I think there is a glitch with msysgit in the 1.8.x versions that exacerbates these symptoms, so another option is to try with an earlier version of git (<= 1.8.3, I think).
via: fatal: early EOF fatal: index-pack failed