It seems that GOG versions only add a working music patch they did not change hardware acceleration compatibility. Users on AMD cards are still reporting issues. Below are the patches wehave created this morning using dgvoodoo which include the graphics fixes for both MotS and JK. Basically its a DDraw wrapper that emulates a older version of Direct3D providing a smooth experience for all users with all graphics cards. This release has been tested on 7/8/10 Preview with AMD & Nvidia cards and is working.
This Fix Does Require a card that supports DirectX 10.1 or higher and Vista/7/8/+
Fix 2: AMD Users
AMD users with drivers 13.1 or higher will experience graphical glitches. Download this and place the 13.1 dll file in your Jedi Knight folder. Make sure this is no other ddraw.dll in the folder.
Fix 3: (Thanks Teleguy & Tarvis) WineD3D
If for some reason you do not have a card that supports DX10.1 or higher or are having issues with the ultimate patch, copy over these dll files in your JK directory. The game will take a long time to load but be patient because it is loading. (The zip contains both JK and JKM.exe)
jkdf2.net/JKBot/JKArchive/JKDF2/Game%20Files/tools/PATCH/ddrawXP.zip (XP Users)
Also if you guys want to play with online with old Zoners or the multiplayer community please visit JKDF2.net , It also has a huge files archive with over 2000 JK MP maps , mods and more. The JK'ers are located on the JK IRC link on the left navigation panel on the homepage.
You guys, since for me and for other people that the links don't work. I found them here!