I suggest you to post some extra data...
- Your systems specs.
- Operating system.
- DOSBox version.
- Configuration of DOSBox.
But, I think you have more problems than DOSBox.
DOSBox does not change your system configuration... or at least it is unrelated to you DOS prompt problem (I assume you are referring to cmd or command window).
Also DOSBox does not run any Windows program. It is possible, though, install Windows 3.0 or 3.1 on DOSBox and run some Windows programs, but DOSBox doesn't run Windows programs alone.