As I found out myself from Jesse, different project categories have different uploading permissions with respect to file sizes and types. List your project type and make some suggestions and I expect they will work them in.
Hmmm ... my Project is listed as an "End User Module", so I guess I can see why the list of allowable uploads is the way it is ...
I can't seem to change the category on edit, however. So please add .zip to the list of allowable download types? Worst case, I can delete and re-create the project.