When you're having issues like that, you should really talk to me as soon as you're having the issue. You don't have to open and close it all the time.
Virtual Files can keep separate configuration files per "character" automatically, different from the one you launch normally. When you use the Quick Setup Wizard (which it sounds like you are avoiding, and that's fine), this is one of the things it does for you automatically depending on the game. For EVE, it keeps a separate prefs.ini (which stores video and other settings) and core_public__.dat (which stores the last login name). The only thing you need is a custom prefs.ini that is set to full screen, for ISBoxer, and the normal prefs.ini that is set to windowed, for whatever else.
If you don't want to use the Quick Setup Wizard, that's perfectly fine. There's also a Virtual Files Wizard that will set up the same virtualization for your existing ISBoxer characters. Right click Virtual Files in the top pane and select Virtual File Wizard, then there's a drop-down box to select the game (EVE) and then you pick the characters to apply it to. Voila, instant separation of config files and zero reason to launch the game, change the setting, close the game, launch ISBoxer, then launch other game instances. I would not recommend doing what you're doing to anyone at all.
Annoying to the point i dont use it anymore. Like I said when you fix it I will subscribe again but its been months and no development or atleast none from what I can see.
That would, indeed, be annoying. If you'd like to try it the recommended way I've added some subscription time to your account -- feel free!
As far as development, I've done tons of Inner Space updates since you purchased a subscription in October, not to mention ISBoxer 38 was in public beta and heavy development from December until it was released in February. ISBoxer 38 was a massive update. I'm not sure what else, besides fixing this bug in specific, you want me to do development-wise! Also, I provide support nearly every waking hour via the ISBoxer Chat Room.