#37 shows that modules may have unique file requirements. In that case, .pyc files needed to be included in zips being uploaded to ShotGrid. Some tool developers use .pyc files as a crude-form of antipiracy and don't ship .py files with their tools. In the case of cpenv, I was trashing all .pyc files when creating the zips.

The most recent release has a temporary fix just for the case of .pyc files. But a more permanent solution would be to add support for .ignore files in modules. These would behave exactly like a .gitignore file and exclude files based on patterns when publishing modules. This would give control to module authors over which files to include when publishing and stop edge cases from becoming problematic.