"we make too much money to have a deductible ira. so my client"

We? Your Client? We or your client? Whose tax return is this?

"made an ira non deductible ira and immediately switched it to roth."

It's a Conversion, but nontaxable, because the IRA amount already went in post-tax. As long as it was done quickly, there are no earnings to tax. As long as there are not other amounts in other deferred accounts, this is nontaxable.

Over all other accounts. Not just this one account.

"This is the backdoor roth as is described in all of the literature. We have done this every year in this software and it has worked....i just can't get it to work this year"

Read this article:

https://proconnect.intuit.com/community/individual/help/proseries-form-1099-r-faq-s/00/4853