I'm in the same boat. We filed and paid on 4/15. Here we are in June and the IRS website is still showing payment as "pending" and we just received a CP14 letter saying we owe them PLUS penalties now. I've been on hold trying to talk to someone to see what we should do. I can clearly see it's been paid through our bank - they were happy to take our money the same day. 🙂
