I have noticed an issue when using the new Loader that seems to happen a lot. Whenever I use it, the latency fix stops working. Like, it's not loading the same resources as War2Launcher.bat which is war2patcher, etc. Please make sure the loader is running the following in some manor, either by command line or via system calls:
start war2ppatcher.exe -a -f -se -ir -i0 -w
War2noCDloader.exe