@Juschi the skip button skips the version, and it should not prompt again. We have done several updates recently, which have critical fixes for Windows updates, so you will be prompted for them one by one.
The trouble with maintaining f.lux is that we do feature updates sometimes, but we do compatibility updates often as we're glued between the operating system and a bunch of third party drivers. If we had to explain to each person why they should update we would be having millions of conversations about it all the time.