Hello sdaste,
It's a long shot, but was the zip file automatically renamed by the OS to Bpod_Gen2 (1).zip? This could happen if there is already a Bpod_Gen2.zip file in your downloads folder.
Please try clearing any Bpod_Gen2 files in /Downloads/, re-download and extract, clear the old instances from the MATLAB path, add the new one and try running Bpod again.
Thanks,
Josh