I'm filing for an S corp in New York State. I was told by an attorney that my company name wasn't available in upper/lower case, but the same name could be registered in all caps. That seems strange; can two companies have the same name if one is in all caps and one is in upper/lowercase?
I agree with adjusterjack. If a company has trademark protection for a lowercase name, the protection extends to the uppercase version of the name.
I recommend that you choose for your corporation a name that no one else has - one that is unique to you alone. You will want to check the USPTO database, your state database and do an online search, or hire a search firm, to best ensure you are not infringing on anyone else's trademark rights.
I also suggest you speak to an attorney for advice and direction in forming your S Corp - and it should be an attorney different than the one you spoke to previously.