Running Deployed App from command line vs. clicking on exe file

There are two ways to run a deployed application. First, you can double-click on the executable. Second, you can call it from the windows command prompt. When you call it from the command prompt, you get a dump from the Command Window including errors, etc. Typical call would be: cd path software.exe

When open the software by double clicking on it, it behaves differently than when I run it from the command prompt. Does anyone know why this might be the case? I can't even get the errors because it works correctly when running it from the command prompt.