Jong,
One of the workshop participants just uploaded a shapefile that doesn't get extracted but has a prj, name the same as inner files, no collection inside. I've duplicated it at http://sead.ncsa.illinois.edu/acr/#dataset?id=tag:medici@uiuc.edu,2009:data_LPXspBsI-P-MX4x7wXdpNg - can you see what the issue is and suggest a fix/workaround? If you find an answer, let me know and I'll get it deployed for the umbio instance.