Make sure you aren't uploading /platforms or /plugins directories, and that you have one and only one config.xml file in your zip file.
Also, try using another archiver like 7zip just to rule out your archiving tool.
I'm attempting to do what's described in this blog post, which doesn't mention config.xml - Flare projects don't have /platforms or /plugins directories.
I've no experience with Flare itself, but you should definitely have a config.xml file in your project, at minimum so that you can specify the name, app ID, and supported platforms. I can't promise that this is your issue or not, but I would definitely add a config.xml.
Have you tried a different zip tool to see if it behaves?