First of all, I'm glad that your initial problem was solved.
As for the options not seeming to be persisted: Hmm, interesting. The form's closing event calls a method that writes preferences to file. One portion of the code writes these three options as follows:
StreamWriter sw = new
int i = 0;
i = (
launchWhenSystemBootsToolStripMenuItem.Checked == true) ? 1 : 0;
sw.WriteLine("startWithWindows|" + i.ToString());
i = (
showTheSplashScreenToolStripMenuItem.Checked == true) ? 3000 : 0;
sleep_delay = i;
sw.WriteLine("splashDuration|" + sleep_delay.ToString());
i = (
showDidYouKnowToolStripMenuItem.Checked) ? 1 : 0;
sw.WriteLine("showDidYouKnow|" + i.ToString());
So, in each case, at program startup, these integer values are read from file and converted to menu options being either checked or unchecked.
I'd open the program's AppData folder and try an experiment. Open the program normally and enable these three options, then exit the program normally and examine the three relevant files in the AppData folder. Launch the program normally again (using the installed shortcut rather than a startup manager, and NOT minimized to tray). Disable the options and repeat the experiment. I'm guessing that there's something you're doing as a power user
that average users aren't doing, that's causing the issue.