I am having exactly the same issue. Quickbooks Pro Desktop.

Bank of America no longer allows you to download QBO files.

When I attempt to set up syncing with Quickbooks Pro Desktop, I get the "Sorry, we've run into a problem. QuickBooks is having trouble connecting to Bank of America - New. Options; Try again later, this is a temporary issue and will be resolved in a day or two."  But I have tried this numerous times over the past several weeks with exactly the same results. 

This is NOT a temporary issue. This appears to be a permanent failure and I suspect the failure originates in Quickbooks.