As it stands now, every time I start the program I must 1st go into Preferences and tell it what things I don't want, like the Overlays. Also the 1st pop-up I get when the program is 1st started. I uncheck the box, Mark all as Read, and yet if I open the program up tomorrow all is back to the way it was. Most annoying.

What operating system are you running?

Seems like your database and settings aren't saved at all.

On Vista/7 check folder %APPDATA%\cYo\ComicRack\

There should be ComicDb.xml and Config.xml there with some relevant content.

Maybe you have something wrong with your UAC settings that forbid ComicRack writing data to this folder?

I am running Win XP Professional (like there's an amateur version).

Something isn't getting saved somewhere when it should be.
Could be a read only setting is somehow turned on.

comicRack itself won't set anything read only however...and how would it even save things to a read only area in the first place.

Is this only happening with the latest .NET 4 install? Did you use the .NET 3 builds prior?

Are you running the program as admin? Was the software installed as an admin? It sounds like, yeah, you don't have write permission so it's not saving settings. I know in newer versions of Windows you don't have write access to anything in Program Files with the default settings but that shouldn't be the case in XP...still, you need to make sure you're admin before you go any further. There's really no other cause for this than lack of access to write the config files.