I did miss that when I read his post but maybe it will make a difference if he disables full screen in the newsettings.dat and not in the prefs file.
OK, so I tried this (still on release 0.603).
Actually I did a lot of testing now with different combinations of the settings in the prefs file and the settings in the newsettings.dat file, and this what I found out:
Fact 1: The newsettings.dat file just contains the settings you make inside the game (when you click on the "Settings" button, make some changes there and then click on "Save"). It really doesn't make any difference whether you disable Fullscreen Mode in the game options or if you edit the file newsettings.dat directly.
Fact 2: The game can work in window mode and it can work in fullscreen mode, BUT: The game only works if it gets STARTED in window mode and it does not work if it gets STARTED in fullscreen mode. If I start it in window mode then all the buttons in the main screen of the game are functioning. Then I can even click on the "Settings" button and set the game to fullscreen mode there (because I don't want to play inside an annoying window), and the buttons STILL work correctly! But only for the current session. When I quit the game while fullscreen mode is enabled, then I have this issue that on the next launch the game will start in fullscreen mode and the buttons in the main window screen won't work.
These are the facts, but because there are two different files that are responsible for whether the game is run in fullscreen or not, things get a little bit more complicated.
Even more so, one of the files, namely the prefs file, seems to be responsible for settings the INITIAL mode at launch time and controlls whether the game is STARTED in fullscreen or window mode.
The other one, newsettings.dat, seems to be responsible for the actual display mode AFTER the launch of the game, from the time on when the main screen becomes visible.
So if for example prefs says Fullscreen 0 and newsettings says UseFullscreen="true" then the game will launch in window mode and will switch to fullscreen after the launch, as soon as the main screen becomes visible. This would be the perfect combination, because in doing so the buttons on the main screen will stay accessible.
The question is, how can this be accomplished.
If there is no prefs file at all or the prefs file has the settings "Fullscreen Mode 0", then the game will launch initially in window mode, and everything will be fine later on.
Then it doesn't matter whether newsettings has UseFullscreen="true" or "false" (I prefer "true" because I want to play in fullscreen mode).
The problem is, if I delete the prefs file, the game will re-create it every time, and it will contain the settings that correspond to the mode that was set on exit.
For example, I delete the prefs file and set UseFullscreen="true" in newsettings.dat, then everything should be fine.
Well, I start the game, in starts in window mode, switches to fullscreen on the main screen, and the buttons can be clicked. Perfect!
But in the meanwhile the game has already created a new prefs file. As long as I don't exit the game, this new prefs file contains "Fullscreen 0" (which means non-fullscreen). But as soon as I quit the game, it updates "Fullscreen 0" to "Fullscreen 1" (which means fullscreen) in the newly created prefs file, even if I didn't touch any of the settings inside the game.
If I set the options to Fullscreen Off inside the game before I quit it, then the prefs file will have "Fullscreen 0" even after the exit of the game.
So if I want to use fullscreen mode, it doesn't matter if I set it directly in the game options or if I edit newsettings.dat manually. In both cases I need a workaround so that the game will work also on the next lanuch. And these are my possible workarounds:
1. I can delete the prefs file every time before I launch the game or
2. I can set it back to window mode BEFORE I quit the game and set fullscreen again after the next launch (and of course don't forget to set it back to window mode before I exit it again, ...)
So I guess the only thing you would have to do to make it work "out-of-the-box" would be to prevent the game from updating the prefs file everytime the game exits.