That is the only way to get Windows to boot into safe mode. You have to use the boot manager and set the safeboot flag.
That is how msconfig does it and the bcdedit command.
When you tell my program to reboot into safe mode it writes to its settings.ini file that you asked it to. Then when you open windows repair in safe mode it see that setting and then runs the command to remove the safe boot switch.
When you went into safe mode did you ever run Windows repair? I am also going to be redoing the main window in a future update, there is simply to much text on the main window, making it cluttered, so I am going to move the text to a help file. Along with that I will have a lot more info int he help file including the commands and such to make windows stop booting into safe mode
Shane