Resolved in: WPML Multilingual CMS 3.6.0
When you have set up WPML in the main site of a WordPress multisite network, and you then complete a WPML setup in another subsite of this network, then the first site in the network may lose status that the setup has been completed, for the main site.
You can complete the setup wizard in the main site. The settings may be already set, but if they are not you will need to select them again – the number of languages and the languages you need, and then complete the setup.
There should be no further problems unless you complete the WPML setup of another subsite in the network.