Figured this out. Seems the only way to get emails deleted from the server is to use the default Gmail app that comes with the phone. In fact since Gmail comes as a standard app Gmail cannot even be added in to the email section since its already added to the phone and will come back as incorrect username or password.
Now a new problem has come up. I have Gmail alone on its own app and hotmail and aol added to the email accounts and have hotmail added as the default account. I sent a message to AOL from Gmail and replied to the message from AOL but the reply came FROM AOL instead of hotmail. I have hotmail set as the default so should the reply not have been sent by hotmail instead of AOL since hotmail is the default account?