Creating a plugin install zip file with valid headers

Could someone explain to me the etiquette of creating a plugin? I have a plugin that for the last five months has done fine. Then I expanded and required more files. To keep it better organized, I put the non-core files into a sub-folder. When I ZIP it up and install it onto another WordPress install, I get the error: “Invalid Headers” and the plugin won’t activate.

This only happens when…

• Installing from a ZIP file. FTP works fine.
• Trying to activate it after the plugin is uploaded via ZIP. If I go to my plugins page instead and click activate, everything goes fine.

I read somewhere online that WordPress cannot handle ZIP files with sub-folders. Is that true? It seems to me that large plugins like WooCommerce work fine. So why doesn’t mine?

I greatly appreciate any insight you can give! Thanks ??