Although others have already raised the zip issue I feel my contribution brings enough new information to justify a new answer.
I recently faced the same issue. I created my Kodi plugin on a MacBook Pro (El Cap v10.11.1, Late 2013) and zipped the directory via Right-Click --> Compress
and everything worked fine. I then started working on a different MacBook (El Cap, v10.11.2, Late 2013), made some changes and created the zip file the same way and I started getting the error.
After a few frustrating hours it occurred to me to analyse the zip structure. I used the following command: $ zipinfo script.service.autorun.zip
and this is what I got:
// v10.11.1
Archive: script.service.autorun.zip 1376 bytes 4 files
script.service.autorun/
script.service.autorun/addon.py
script.service.autorun/addon.xml
script.service.autorun/changelog.txt
4 files, 1328 bytes uncompressed, 646 bytes compressed: 51.4%
// v10.11.2
Archive: script.service.autorun.zip 3060 bytes 10 files
script.service.autorun/
script.service.autorun/addon.py
__MACOSX/
__MACOSX/script.service.autorun/
__MACOSX/script.service.autorun/._addon.py
script.service.autorun/addon.xml
__MACOSX/script.service.autorun/._addon.xml
script.service.autorun/changelog.txt
__MACOSX/script.service.autorun/._changelog.txt
__MACOSX/._script.service.autorun
10 files, 2222 bytes uncompressed, 1230 bytes compressed: 44.6%
So, obviously, something changed in v10.11.2 but I couldn't find any documentation about it.
The solution for me was to manually zip the directory:
zip -r script.service.autorun.zip script.service.autorun/
Hope this helps!