I downloaded the server off the website, and here is what happens when I start it up
(I tried removing rail craft from the mod folder and the problem persisted but with a different mod and different fml version)
I included the crash report also
21.08 11:23:06 [Server] SEVERE This crash report has been saved to: /./crash-reports/crash-2013-08-21_11.23.06-server.txt
21.08 11:23:06 [Server] INFO at fy.run(SourceFile:849)
21.08 11:23:06 [Server] INFO at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:458)
21.08 11:23:06 [Server] INFO at ho.c(DedicatedServer.java:64)
21.08 11:23:06 [Server] INFO at cpw.mods.fml.common.FMLCommonHandler.onServerStart(FMLCommonHandler.java:350)
21.08 11:23:06 [Server] INFO at cpw.mods.fml.server.FMLServerHandler.beginServerLoading(FMLServerHandler.java:86)
21.08 11:23:06 [Server] INFO at cpw.mods.fml.common.Loader.loadMods(Loader.java:461)
21.08 11:23:06 [Server] INFO at cpw.mods.fml.common.Loader.sortModList(Loader.java:238)
21.08 11:23:06 [Server] INFO cpw.mods.fml.common.MissingModsException
21.08 11:23:06 [Server] SEVERE Encountered an unexpected exception MissingModsException
21.08 11:23:06 [Server] INFO at fy.run(SourceFile:849)
21.08 11:23:06 [Server] INFO at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:458)
21.08 11:23:06 [Server] INFO at ho.c(DedicatedServer.java:64)
21.08 11:23:06 [Server] INFO at cpw.mods.fml.common.FMLCommonHandler.onServerStart(FMLCommonHandler.java:350)
21.08 11:23:06 [Server] INFO at cpw.mods.fml.server.FMLServerHandler.beginServerLoading(FMLServerHandler.java:86)
21.08 11:23:06 [Server] INFO at cpw.mods.fml.common.Loader.loadMods(Loader.java:461)
21.08 11:23:06 [Server] INFO at cpw.mods.fml.common.Loader.sortModList(Loader.java:238)
21.08 11:23:06 [Server] INFO cpw.mods.fml.common.MissingModsException
21.08 11:23:06 [Server] SEVERE The mod Railcraft (Railcraft) requires mod versions [Forge@[6.6.0.516,)] to be available
21.08 11:23:06 [Server] INFO Forge Mod Loader has identified 89 mods to load
21.08 11:23:04 [Server] INFO Searching /mods for mods
21.08 11:23:04 [Server] INFO Completed early MinecraftForge initialization
21.08 11:23:04 [Server] INFO Replaced 84 ore recipies
21.08 11:23:04 [Server] INFO MinecraftForge v6.6.0.515 Initialized
21.08 11:23:04 [Server] INFO MinecraftForge v6.6.0.515 Initialized
21.08 11:23:04 [Server] INFO Attempting early MinecraftForge initialization
21.08 11:23:04 [Server] INFO Starting minecraft server version 1.4.7
21.08 11:23:03 [Server] INFO 27 achievements
21.08 11:23:03 [Server] INFO 210 recipes
21.08 11:23:01 [Server] INFO Adding Accesstransformer map: nei_at.cfg
21.08 11:23:01 [Server] INFO Adding Accesstransformer map: temp.dat
21.08 11:23:01 [Server] INFO Adding AccessTransformer: chickenchunks_at.cfg
21.08 11:23:01 [Server] INFO Adding Accesstransformer map: codechickencore_at.cfg
21.08 11:23:01 [Server] INFO Found valid fingerprint for Minecraft Forge. Certificate fingerprint de4cf8a3f3bc15635810044c39240bf96804ea7d
21.08 11:23:01 [Server] INFO Adding Accesstransformer map: pcc_at.cfg
21.08 11:23:01 [Server] INFO Download complete
21.08 11:23:01 [Server] INFO Downloading file http://files.minecraftforge.net/fmllibs/bcprov-jdk15on-147.jar
21.08 11:23:01 [Server] INFO Download complete
21.08 11:23:01 [Server] INFO Downloading file http://files.minecraftforge.net/fmllibs/asm-all-4.0.jar
21.08 11:23:01 [Server] INFO Download complete
21.08 11:23:00 [Server] INFO Downloading file http://files.minecraftforge.net/fmllibs/guava-12.0.1.jar
21.08 11:23:00 [Server] INFO Download complete
21.08 11:23:00 [Server] INFO Downloading file http://files.minecraftforge.net/fmllibs/argo-2.25.jar
21.08 11:23:00 [Server] INFO Initialized
21.08 11:23:00 [Server] INFO Forge Mod Loader version 4.7.22.539 for Minecraft 1.4.7 loading
21.08 11:22:59 [Server] INFO /usr/bin/java $START
21.08 11:22:59 [Multicraft] JAR file not found, copying from global JAR directory
21.08 11:22:59 [Multicraft] Loaded config for "Default"
21.08 11:22:59 [Multicraft] Starting server!
21.08 11:22:59 [Multicraft] Loading server properties
21.08 11:22:59 [Multicraft] Received start command
(I tried removing rail craft from the mod folder and the problem persisted but with a different mod and different fml version)
I included the crash report also
21.08 11:23:06 [Server] SEVERE This crash report has been saved to: /./crash-reports/crash-2013-08-21_11.23.06-server.txt
21.08 11:23:06 [Server] INFO at fy.run(SourceFile:849)
21.08 11:23:06 [Server] INFO at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:458)
21.08 11:23:06 [Server] INFO at ho.c(DedicatedServer.java:64)
21.08 11:23:06 [Server] INFO at cpw.mods.fml.common.FMLCommonHandler.onServerStart(FMLCommonHandler.java:350)
21.08 11:23:06 [Server] INFO at cpw.mods.fml.server.FMLServerHandler.beginServerLoading(FMLServerHandler.java:86)
21.08 11:23:06 [Server] INFO at cpw.mods.fml.common.Loader.loadMods(Loader.java:461)
21.08 11:23:06 [Server] INFO at cpw.mods.fml.common.Loader.sortModList(Loader.java:238)
21.08 11:23:06 [Server] INFO cpw.mods.fml.common.MissingModsException
21.08 11:23:06 [Server] SEVERE Encountered an unexpected exception MissingModsException
21.08 11:23:06 [Server] INFO at fy.run(SourceFile:849)
21.08 11:23:06 [Server] INFO at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:458)
21.08 11:23:06 [Server] INFO at ho.c(DedicatedServer.java:64)
21.08 11:23:06 [Server] INFO at cpw.mods.fml.common.FMLCommonHandler.onServerStart(FMLCommonHandler.java:350)
21.08 11:23:06 [Server] INFO at cpw.mods.fml.server.FMLServerHandler.beginServerLoading(FMLServerHandler.java:86)
21.08 11:23:06 [Server] INFO at cpw.mods.fml.common.Loader.loadMods(Loader.java:461)
21.08 11:23:06 [Server] INFO at cpw.mods.fml.common.Loader.sortModList(Loader.java:238)
21.08 11:23:06 [Server] INFO cpw.mods.fml.common.MissingModsException
21.08 11:23:06 [Server] SEVERE The mod Railcraft (Railcraft) requires mod versions [Forge@[6.6.0.516,)] to be available
21.08 11:23:06 [Server] INFO Forge Mod Loader has identified 89 mods to load
21.08 11:23:04 [Server] INFO Searching /mods for mods
21.08 11:23:04 [Server] INFO Completed early MinecraftForge initialization
21.08 11:23:04 [Server] INFO Replaced 84 ore recipies
21.08 11:23:04 [Server] INFO MinecraftForge v6.6.0.515 Initialized
21.08 11:23:04 [Server] INFO MinecraftForge v6.6.0.515 Initialized
21.08 11:23:04 [Server] INFO Attempting early MinecraftForge initialization
21.08 11:23:04 [Server] INFO Starting minecraft server version 1.4.7
21.08 11:23:03 [Server] INFO 27 achievements
21.08 11:23:03 [Server] INFO 210 recipes
21.08 11:23:01 [Server] INFO Adding Accesstransformer map: nei_at.cfg
21.08 11:23:01 [Server] INFO Adding Accesstransformer map: temp.dat
21.08 11:23:01 [Server] INFO Adding AccessTransformer: chickenchunks_at.cfg
21.08 11:23:01 [Server] INFO Adding Accesstransformer map: codechickencore_at.cfg
21.08 11:23:01 [Server] INFO Found valid fingerprint for Minecraft Forge. Certificate fingerprint de4cf8a3f3bc15635810044c39240bf96804ea7d
21.08 11:23:01 [Server] INFO Adding Accesstransformer map: pcc_at.cfg
21.08 11:23:01 [Server] INFO Download complete
21.08 11:23:01 [Server] INFO Downloading file http://files.minecraftforge.net/fmllibs/bcprov-jdk15on-147.jar
21.08 11:23:01 [Server] INFO Download complete
21.08 11:23:01 [Server] INFO Downloading file http://files.minecraftforge.net/fmllibs/asm-all-4.0.jar
21.08 11:23:01 [Server] INFO Download complete
21.08 11:23:00 [Server] INFO Downloading file http://files.minecraftforge.net/fmllibs/guava-12.0.1.jar
21.08 11:23:00 [Server] INFO Download complete
21.08 11:23:00 [Server] INFO Downloading file http://files.minecraftforge.net/fmllibs/argo-2.25.jar
21.08 11:23:00 [Server] INFO Initialized
21.08 11:23:00 [Server] INFO Forge Mod Loader version 4.7.22.539 for Minecraft 1.4.7 loading
21.08 11:22:59 [Server] INFO /usr/bin/java $START
21.08 11:22:59 [Multicraft] JAR file not found, copying from global JAR directory
21.08 11:22:59 [Multicraft] Loaded config for "Default"
21.08 11:22:59 [Multicraft] Starting server!
21.08 11:22:59 [Multicraft] Loading server properties
21.08 11:22:59 [Multicraft] Received start command