It's odd that only an In-plan Roth Rollover would be performed on only the pre-tax sub-account in the 401(k), but I'll tax your word for it. The amount shown in box 2a of the Form 1099-R is the taxable amount. With no after-tax basis included in the IRR (nothing in box 5 of the Form 1099-R), the entire amount is taxable.
