Commend Prompt on Windows 8/8.1

Hey Guys I have a problem which occurs on only Windows 8/8.1

Older versions have no problem like that.

Whenever I normally run a script (.bat) file it works fine and it's current directory:

C:\Users\%username%\Desktop>

But if I run the same script as Administrator, it's current directory:

C:\WINDOWS\System32>

In some cases, especially I type code such as ".\" this problem occurs and I can never run it as Administrator.

Any idea why is this happening and how can I get rid of this problem?

My Best Regards

Halim