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We have not had problems before but now our worlds have NO bats at all, hostile mobs spawn in small groups i one kind only (for example a whole ravine had only 6 zombies in it and they all spawned on the same block), animals spawn in either small groups (2-3 of SAME animal) or you have to travel thousands of blocks and find a chunk that is overloaded with animals (but just one chunk). I have been through all the config files and can't find anything that changes the vanilla mobs and spawn rates. It is very weird to not have a single bat spawn in any of our worlds.

We have 1.6.4 and everything is up to date.

These are the mods we have:

bspkesCore
Treecapitator
Furniture Mod (Crayfishes)
Agriculture
Ars Magica 2
Applied Energistics
Aquaculture
Archimedes Ships
Backpack
Bibliocraft
Bibliowoods
Buildcraft
Carpenters Blocks
Computer Craft
ExtrabiomesXL
Extrautilities
Factorization
Mob Dismemberment
Forestry
Hats
IC2 Experimental
Inventory Tweaks
Ironchest
Logistics Pipes
Metallurgy
Minefactory Reloaded
Morph
Mystcraft
NEI
Nether Ores
Open Blocks
Ore Spawn
Pam's Mods
Plant MegaPack
Plugins for Forestry
Portal Gun
Tinkers Construct
Camping Mod
Thermal Expansion
T Mechworks
Twilight Forest
Underground Biomes
Universial Electricity
Waila
Witchery
Zans Minimap
ID Fix