No, you do not need a new 1099R. The program will allow you to enter the numbers separately into what was contributed/rolled where.
Clarifying: one 1099R from a 401k with a basis of after tax dollars plus gain. The after tax dollars were moved into a Roth IRA. The gain was moved into some type of IRA.
If you are having trouble, you may want to contact a specialist that can work through that section of the return with you. It is a very particular process.
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