I am having the same issue as genpatton043.
Running only IFA3 AIO and CUP Terrains Core yields the following (previous entries of other base classes seemingly updating fine omitted):
18:22:52 Updating base class ->ctrlToolbox, by a3\3den\config.bin/Cfg3DEN/Attributes/Toolbox/Controls/Value/ (original a3\3den\config.bin)
18:22:53 Updating base class Mod_Base->, by a3\data_f_destroyer\config.bin/CfgMods/Jets/ (original a3\data_f_jets\config.bin)
18:22:53 Updating base class ScrollBar->ScrollBar, by WW2\MissionsWW2_p\WW2_Gamemodes_SearchAndDestroy_p\config.cpp/RscListNBox/ListScrollBar/ (original (no unload))
18:22:53 Updating base class CfgEnvSounds->CfgEnvSounds, by K9S\K9S_Djalka\config.bin/CfgWorlds/Altis/EnvSounds/ (original CUP\Terrains\cup_terrains_worlds\envsounds\config.bin)
18:22:55 Error updating 'bin\config.bin/CfgWorlds/SWU_Aachen_Outskirts/EnvSounds/CfgEnvSpatialSounds/' by 'WW2\TerrainsWW2_swurvin\Aachen_Outskirts_c\config.bin/CfgWorlds/SWU_Aachen_Outskirts/EnvSounds/CfgEnvSpatialSounds/', base 'CfgEnvSpatialSounds'
ErrorMessage: bin\config.bin/CfgWorlds/SWU_Aachen_Outskirts/EnvSounds/CfgEnvSpatialSounds/: Cannot find base class 'CfgEnvSpatialSounds'
Application terminated intentionally
18:22:55 ../lib/Network/networkServer.cpp ClearNetServer:NOT IMPLEMENTED - briefing!
Class CfgWorlds destroyed with lock count 1
Class SWU_Aachen_Outskirts destroyed with lock count 1
Class EnvSounds destroyed with lock count 1
Class CfgEnvSpatialSounds destroyed with lock count 1
Class CfgWorlds destroyed with lock count 1
Class SWU_Aachen_Outskirts destroyed with lock count 1
Class EnvSounds destroyed with lock count 1
Class CfgEnvSpatialSounds destroyed with lock count 1
bin\config.bin/CfgWorlds/SWU_Aachen_Outskirts/EnvSounds/CfgEnvSpatialSounds/: Cannot find base class 'CfgEnvSpatialSounds'
18:22:56 Critical:Destroying running thread!
18:22:56 Critical:Destroying running thread!
18:22:56 Critical:Destroying running thread!
18:22:56 Critical:Destroying running thread!
18:22:56 Critical:Destroying running thread!
18:22:56 Critical:Destroying running thread!
18:22:56 Critical:Destroying running thread!
18:22:56 Critical:Destroying running thread!
18:22:56 Critical:Destroying running thread!
18:22:56 Critical:Destroying running thread!
18:22:56 Critical:Destroying running thread!
18:22:56 Extensions:
steam@notahostname:~$
This is on Arma3 version 2.12.150301 dedicated server (linux), with up-to-date IFA3 AIO and CUP Terrains Core, nothing else loaded.
Unfortunately it's been quite a while since last we ran a WW2 modpack, so I'm not able to say when this issue started happening.