I think there have been some updates to IPN causing issues. I've started to see this more lately.
My best suggestion is to move to "Express checkout only" instead of paypal standard. It will be essentially the same process, but won't rely on IPN which seems inconsistent and is difficult to debug.
Express only will still allow users to checkout with credit cards and is a free service. Really the only advantage of paypal standard over express checkout is that the coding for express checkout is more complex, but we've done that part for you.
Please give that a try and let me know if you have questions or issues.