What are you uploading to PG Build? I'm guessing you're uploading the project as created from PG Desktop, which is incompatible as-is with PhoneGap Build. You will need instead to place a "config.xml" file inside your "www" directory (adjust file paths as necessary), include your icon/splash assets in the "www" directory as well, and then zip up the contents of your "www" directory and upload this to PGB. Otherwise you'll get incorrect results.
(Side note: never upload platforms/ or plugins/ directories to PGB. You're only asking for trouble if you do.)