I think I got the installation process correct. I grabbed the 792 installer and launched it. Selected the Server option and pointed it to an empty folder. It did its download and I created a .bat file to launch the minecraftforge-universal-1.6.2-9.10.0.792.jar (not minecraft_server.1.6.2.jar).
When I launch the server it starts without problem but it doesn't seem to be loading any mods. So far I've only tried Biomes-O-Plenty and IC2. I did set the server.properties level-type to BIOMESOP but I'm not seeing any of the mods biomes. I also found a swamp biome and found no IC2 rubber trees. I've deleted the world a few times and restarted the server and it all looks vanilla to me.
I do see something in the log about checking the two mod files to see if they are coremods but otherwise, I don't think they are being loaded. I also am not seeing a config folder. Am I missing something? Everything works cherry on the client side.
ForgeModLoaderLog - http://pastebin.com/7d4tWzCe
Update: I installed Iron Chests, I can craft it but can't pull it out of the crafting table. I've triple checked everything and can't figure this one out. Either it's a bug or I'm just stupid. =)