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Only give MC max 4Gb of memory for the starters and try FORCE updating your client for any errors in files. Make backups!

To spawn wither skeletons, you need to place the spawner in Nether. Even normal skeleton spawner placed in Nether will spawn rarely wither skeletons.

Im quite sure, if you remove ATG and lag will be gone. Try that....

Then its quite certain that world is corrupted beyond repair Im affraid...

Your world is probably corrupted, take backup and try opening it with MCEdit. Sometimes you can manage to fix corrupted worlds with MCEdit.

Well, when server is running 20 TPS, its running smoothly. AE2 default import bus for example aint fast until upgraded....

Graphics "lag" and server lag are two different things. If you press F3, how does your FPS fluctuate?

Did you try creating world without your modifications, this would help locating problem, but by looking log, RFTools is trying to create its dimension 21 and its allready there. Did you add any mod that might create dimension?

Looking at log, it seems to try create Twilight Forest biome and that should not happen to my knowledge in creation of Deep Dark. Seems weird!

20 TPS means your server is running perfectly, when it gets under 20TPS, means server has troubles keeping up...

MCEdit should be able to delete wanted entity anywhere, make backups before!

Im guessing your creating chunks as you explore? I had a problem with pre generating world with ServerTools, vanilla biomes dont have any trees/flowers or anything living on them. I saw similar looking errors in log after the generation was done. So there is something fishy on chunk generation...

If not yet, install Fastcraft on server too, it makes creating chunks little bit easier for CPU, but by no means it aint a miracle cure for it.

By quickly checking the log, it seems Chunkloaders are probably the culprit. Either remove the mod and try to start the world so all the chunkloaders are removed from world, then put mod back and restore them as needed in the world back. Or use MCEdit to remove bugged chunkloaders in the world...

Its really hard to help cause you have given so little info yourself. Make sure the mod is .JAR and not zipped file. Do you have compatible graphics card? Even with vanilla, shader mods are EXTREMELY heavy on CPU/GPU, so dont expect to play with it smoothly...

What modpack are you trying to launch? 1.5Gb memory aint enough for new 1.7 packs...

In the past IC2 high tier armor suit also negates wither damage, makes you pretty much invincible till power runs out. Dunno if they have changed it.

Google really is your friend, just search the 2nd line. For example: http://www.minecraftforum.net/forums/mapping-and-modding/minecraft-tools/1261480-minecraft-region-fixer Remember to backup first!

Well, youre not gonna like it, but basicly your world is corrupted and fixing it is real pain and not 100% sure to work either. These lines reveal theproblem: [29/11/2014 12:57:02 PM] [Server thread/ERROR]: Encountered an unexpected exception [29/11/2014 12:57:02 PM]...

Dont post in multiple sub forums is good start to get help!