Seems like a Texture problem so I doubt that it would be SH3 Commander, although I use 2.5, the latter
may change atmosphere.

You may have to backtrack your moves as to whether you installed a new mod, if you use JSGME then takeany mods out, try running SH3 to see if the problem has cleared. Did you change anything external to SH3 Commander (Bios settings, drivers etc) that may have inadvertantly (probably spelt that wrong) cause problems in SH3?