The gpg-agent that ships with GpG4Win is a version 2 gpg agent and only works with gpg2. The gpg in MinGW is gpg 1.x and it doesn't pick up this gpg-agent.
However, everything still works - you just have to enter your password for each file you decrypt. Slightly onerous but not a huge deal breaker.
I notice there is away to specify your own gpg versoin in the _blackbox_common.sh file but I don't really know how that works. If someone were to specify to use gpg2 then they could probably use the agent in Gpg4Win but I don't know and don't know how to test that.
Older git for windows MinGW didn't support updating the plain text files in keyfiles/live/blackbox-admins.txt and blackbox-files.txt due to an error `cannot make pipe for process substitution function not supported`
The newer version of Git (which is also more secure) also resolves this issue.