I've had that size annoyance on some older games, I think Virtual Villagers was one of them that weren't coded on exit to return to your orig settings. Played on 800x600 I guess. If I had Outlook Express running in the bg and checked mail, it was all blown out, half the toolbar icons off screen. Icons too. I've spent many hours getting all my ducks back in a row, I'm a stickler for design and organization too. Then I learned if I just restarted pc after a game everything is back to normal. Or, close OEx and reopen it, it was back to right settings.
I am surprised DireGrove does that. Seems on my vista laptop I saw some option setting somewhere to select if you wanted progs to return your settings. Where I don't know, maybe Appearance? I can't find or remember anything on Vista, I just play games on it with a mini mouse. Hate typing on it, got a short KB but a hassle so still do everything else on pc XP. I wish I could downgrade my laptop to XP where I can usually figure things out.