Ok ,the application named GNS3 when you package it ,it wont run ,but if running from inside %ProgramFilesDir% it runs !!!

Hi all, as my title is self explanatory many applications wont run if they are packaged,but amazingly they do run if you dont package anything and run the .EXE from  within the %ProgramFilesDir%, and the well known application called GNS3 is a good example of what I am saying . Am I missing something ? thanks for every help.