"But the distributor is now saying that the box to roll over to a traditional IRA was checked"
What does box 7 show? THIS is what you need to look at!
Did you document your conversion with the agent?
How do you know it was a Roth rollover vs a traditional rollover? Did the client give you any documentation that stated either??
IF the financial institution stated it was a rollover to an IRA account, hence the taxable amount is Zero, then leave it at that.
IF you know that the amount was "actually" rolled over into a Roth IRA, then, yes, then the distribution amount "should" be taxable.
Too many IF's!
Yes, there "may" be a matching problem so you need to look at your client's docs to figure out how to correctly categorize the rollover.
Then include an explanation with the return explaining what happened. You may even include a statement explaining that the financial institution will not amend the 1099-R hence the matching issue.
FYI...
Almost all financial institutions will NOT issue a corrected 1099-R IF the client had closed the account and left the institution.
Even if the client had not closed the account, it's still very difficult in getting a corrected 1099-R since it could takes months (Literally! based on my experiences with major financial institutions with my clients!) before it's issued.
Good luck!