Packages rebuilding:
1st: Be sure that, in deusex.ini, Paths=..\TNM\system\*.u is up to Paths=..\System\*.u (in core.system) 
2nd: Delete all packages WHICH you want to compile before compiling

[Core.System]
PurgeCacheDays=30
SavePath=..\Save
CachePath=..\Cache
CacheExt=.uxx
Paths=..\TNM\system\*.u
Paths=..\System\*.u

Compile the files in this order:

EditPackages=Core
EditPackages=Engine
EditPackages=Editor
EditPackages=Fire
EditPackages=IpDrv
EditPackages=UWindow
EditPackages=UBrowser
EditPackages=Extension
EditPackages=DeusExUI
EditPackages=DeusExConversations
EditPackages=DeusExSounds
EditPackages=DeusExItems
EditPackages=DeusExDeco
EditPackages=DeusExCharacters
EditPackages=MPCharacters
EditPackages=DeusExText
EditPackages=IpServer
EditPackages=DeusEx
EditPackages=UBrowser
EditPackages=DXOgg
EditPackages=precipitation
EditPackages=CaroneElevatorSet
EditPackages=ConSys
EditPackages=UMenu
EditPackages=UWindow
EditPackages=TNMNative
EditPackages=TNM
EditPackages=TNMDeco
EditPackages=TNMCharacters
EditPackages=TDP
EditPackages=TDPDeco
EditPackages=TDPText