Ok, I found where the problem lies with the PayPal IPN contribution. In reality, there's no real "conflict"; it's just a simple email being sent in text format instead of HTML. The place to make the necessary changes lie in "Order.class.php" (under 'includes/modules/payment/paypal/classes/osC/', line 220~). Although, the changes are not that simple because the PayPal OSC Order class is missing a few globals to make everything work (looks like the module is pretty self-contained...). It's not going to be hard, but a bit lengthy (for me anyways) since I'm not an expert PHP coder.
I have an idea on how to fix this problem, but the changes I have planned are not efficient. It's going to be more of a hack than a fix; a lot of hardcoding might be involved, but I'll do my best to eliminate that kind of mess. I'm still looking over the code...