I don't know what exactly it is but it looks like starting via "direct launch" is mixing up the code.
For example I replaced the loginscreen but with the same resource name, just in a different jar file. when launched outside steam (directly) everything's fine.
But on steam I had to rename the resource.
There are also strange bugs where on my steam release the distance to a quest giver is not displayed while it is on non steam version.
I'm using the exact same build so it's not that.
In any case I'll probably migrate to chained launch soon. '
Would be cool to hear if anyone else had some trouble with their direct launch approach or if I am doing something wrong, which I kind of hope.