A few times in the last month I've lost my subscriptions to threads, so that I don't recieve an e-mail notification when a new post is added. I will get the notifications like normal but then all the sudden nothing. After a day or two, I'll check the thread, and sure enough there are a bunch of new posts to read. And at the top of the thread, it still says "remove subscription", so according to RCU I am still subscribed to the thread(just not getting notification of new replies).

I am not sure if it is something I am doing or if it's a problem with the website?

your isp or mail client is blocking the notices.

So, you're saying my ISP thinks the notifications are spam??