It may be something specific to your installation or project. I've just tried Exporting a project, un-zipping to a different path and it Compile Ok.
Export to Zip certainly is selective of which folders are saved. In my case, under 'Objects' the 'bx4libs', 'bin' and 'gen' folders are not included. As are 'layout', 'xml' and 'source' under the 'res' folder.
If your project places/expects files in those folders, a Zip obviously won't work. And you probably shouldn't be putting / expecting files in those folders!