Hi Lakshmi,
Both languages are good for automating desktop applications and it is irrelevant what language was used to create the tested application itself.
Both languages have their pros and cons, but these pros and cons are cases of personal preferences and while one can treat some case as a complete showstopper another one will not even mention it.
So, as both these languages are new for you, I would recommend to consider things like: what language I prefer to know; for what language it will be more easy to find a people for my team later; what language will be more convenient for the use in other test projects (code reuse) (VBScript is the worst choice for testing Web Services, for example); etc. and make your decision based on the answers been made.
P.S. I expect that there will be quite a lot of replies in favor of JScript... Maybe guys will mention something that will really matter to you, but as I said, both languages are equal as for the functionality provided and everything you will need for your tests can be implemented using any of these languages.