When I go into the setup options under the root folder both screen resolution and mip mapping options will not save. No mater what i pick every time I start the game it keeps defaulting back to 800x600 res and all mip mapping options back to normal. I'm using D3D not Glide.

So you're using the setup program directly and not the shortcut in the start menu? Assuming that's the case, that's the problem. There are some command line options set in the start menu shortcut that have to be there or the program won't apply the setting properly.

I don't have the games installed at the moment so I can't give you a step by step on how to find the shortcut you need, but I'll get one installed later and get back to you if you need the help.

I spent some time last night figuring out this issue. I was able to resolve it by directly editing the .conf file in the game directory, in my case located in \GOG.com\Ultima Underworld 1 and 2

I was trying to get Ultima Underworld running fullscreen in a 4:3 aspect ratio, and had no luck using the Graphic Mode Setup application. Manually editing \GOG.com\Ultima Underworld 1 and 2\dosboxULTIMA1.conf allowed me to make changes that didn't seem to stick otherwise. Make sure you check out dosbox_README in the DOSBOX folder; it details the options for all the different lines in the .conf file.