Unfortunately, I think the program often has difficulty with this situation.

Have you tried a direct override, by doing a RIGHT-click on the entry fields and selecting "override"?  Unfortunately, that might the best way to deal with it.

Doing overrides MIGHT required you to "disable error checking" when you e-file the tax return.  To do that, you need to e-file it from HomeBase (you can't do it when e-filing when the client file is open).