For anyone having problems installing mods on Windows through the Launcher (mods not showing up in the game's launcher, see my post above) : make sure you're using the default location for your "My Documents" folder. I had remapped mine to another drive and it broke the mod installation process. Reverting it to the default location (ie. %USERPROFILE%\Documents\) fixed the problem. It looks like the path is hardcoded, or at least not dynamic.
Stirling work locating the source of the problems! Bugfix for that should be in the next release.