As for the transactions not showing on your PayPal profile this should only be occurring if you have the store set to test mode, or perhaps the sandbox. I think you would know if you were using the Sandbox credentials though. Check on the test mode setting in your globals file and make sure that it is set to false like this:
$WAGLOBAL_Test_Mode = false;
Hi Eric, didn't know if you saw my post as well, or just needed more time for the deeper detail?