I'm not really a Linux user, so this is a shot in the dark: did you try changing the "output" setting? Are you sure your graphics adapter is configured correctly in Ubuntu (3D acceleration enabled, OpenGL available, etc.)? If your output method doesn't support scaling all the other settings will have no effect on the size (number of pixels) of the output.

OpenGL would be an output to use on Linux for fullscreen - that should get you the image filling the screen with filtering.

-Frob

Spent some more time digging around and found another unrelated problem using surface output with a scaler. changed to overlay and turned the scaler off, now I get a full screen image. Problem is the games run much slower, there is an apparent lag to gameplay, and the images are really choppy.

Not really well versed in tackling hardware config in linux so there is a possibility of vcard issues. I'm still looking into it. May explain why it worked perfectly on my previous OS install.

I tried switching the output to opengl previously and that slowed things down even more. Couldn't even use it. I've also tried increasing frameskip and cpu cycles are maxed with no luck. Should mention though, game runs near perfect in small window, just has issues when going to full screen. Hope this helps.