Run launcher.exe, with both launcher.exe and fs2_open_r.exe in the root FS2 directory. Select fs2_open_r.exe as the freespace executable in the launcher (by hitting browse and selecting it) and go to the video tab, select DX8, and change your resolution to 1024x768. Also, some of the later builds don't seem to work correctly in normal DX8, so add the tag -htl to the command line in the launcher to enable ht&l. Press "Apply" to set your registry up as it should be, and then press "Run" to launch the game. There were a few builds that didn't work if not started directly from the launcher, and since I'm not positive that this has been corrected you're probably best off setting it up this way each time you play. It's a little buggy, but that's the general gist of it.
