Well, that setting is set to false. Interesting, I assume you're persisting GUI control settings directly, and this is a checkbox somewhere in options? When I opened the Options dialog to check, in the Startup/Shutdown section, I noticed neither Start with Windows or Start Minimized are checked -- yet it does start with Windows! I've not added it manually to the Startup group or the registry, but it's there in HKCU\Software\Microsoft\Windows\CurrentVersion\Run, even without these startup checkboxes checked.
Do you think this weirdness could be related?
The ScreenshotCaptor.ini file has a Last Modified date of November 18, 2008. So I check the setting to startup with Windows and exited SSC, but the file modified date didn't change -- could it be writing the file elsewhere? According to the ConfigDir.ini, the default is to store settings in the app folder, and I haven't told it otherwise.