Filing this for future reference, right now MultiUpload's so broken under MW 1.26+ that it's not even funny...
MultiUploadApiUnpack::unpack (in MultiUploadApi.php) hard-codes certain shell commands, namely the usage of tar or unzip to untar/unzip a .tar/.tar.gz/.zip file. This works well on most *NIX-like systems where said binaries are available, but not so much on Windows. Windows users should have a way to configure MultiUpload to use 7-Zip instead.
Related StackOverflow thread about unzipping files via CLI on Windows