Are you detecting some IRS schizophrenia there? 

"Direct deposit is the only way to go!"  

"Oh, by the way, we won't allow it for some returns."

I think the problem they have is making sure the funds get into the right account.  Banks may not feel comfortable matching names.  Also, trust companies would be asking for hundreds of payments to go to the same account, and IRS won't allow more than three.