I am having a similar issue. While my e-invoice payments are being charged the 2.9% as promised, my keyed payments are being charged 3.4% rather than the 3.1% ProAdvisor rate I was promised. I am on the phone with them as we speak. I found transparent posted pricing for all methods for ProAdvisors here: 

https://quickbooks.intuit.com/accountants/products-solutions/merchant-services/ 

I am hoping that this article coupled with the email I have from sales quoting these same numbers will get me somewhere.