Yes, I have the same problem with one trust, and my partner in the firm has a similar case. You are not alone. This seems to be an issue only with the IRS service center that processes trust tax returns.
And to add insult to injury in my case, the client just received a notice from the IRS, saying that they hadn't paid the amount due with the trust return when filed! I advised my client to simply wait - Hopefully the IRS employees will find these tax payment checks when they get back to work in their offices.