running exe file from matlab doesn't work properly

I have a executable file that I want to run through Matlab. I used the command system to do it. It works well, so Matlab opens correctly the .exe file showing its interface in the Matlab's command windows. However it cannot run appropriately the commands of the .exe itself. If I run the same commands without using Matlab (using its own interface) it works fine. It seems like there is some subtle difference in the cmd environment that is invoked by Matlab but I cannot understand what. Any suggestion?