Based on what you said in your post, this sounds like an issue that is only affecting your Method Account. For an issues like this, I would suggest calling in to our Support line so that we can troubleshoot over the phone with you and doing some testing. I am not aware of any changes on our in regards to this.
Either call the us at 1-888-025-6238x2, or you can send me an email with your Company Account name and Contact info, and I will give you a call back. You can either email me privately through the forums, or at firstname.lastname@example.org. We would also likely need access to the Method User that is unable to send emails.