I have everything running on windows in msys/bash/emacs with lein and cmd.exe with lein.bat. But I also have all the appropriate GNU tools installed and working enough to build with gcc/g++. So my install is relatively complete and probably not typical considering the time it took to get to this point.

I ran into problems where lein.bat didn't work in powershell or msys. This is commonly the case so I didn't think it warranted any bug reports. It did take some additional effort but it was similar to the effort required to get just about anything working in clojure.

For the record my take is this is a Microsoft problem. They need a packaging system that works and is built with all the crazy native windows development quirks in mind. See http://coapp.org/