Structure of Installation Root: /bin/*.dll, myapp.exe /lib/*.jar, myapp.jar /jre Working directory - bin If you will run myapp.exe it launch "../jre/bin/javaw" -jar "../lib/myapp.jar", but it was create process in wrong directory - lib, instead of bin. For example: Here is right command from right directory: C:\Program Files\My Corp\My App\bin>"../jre/bin/java" -jar "../lib/myapp.jar" (here all works OK) Here is wrong command from right directory: C:\Program Files\My Corp\My App\bin>myapp.exe (here does not load any bin*dll native librs from current directory)