You didn't answer my question about whether you are using TurboTax Online or the CD/Download TurboTax software. I'm not sure what you mean by "using the same program." Since you are preparing two tax returns, I hope you are using the CD/Download software. If you are using TurboTax Online you cannot prepare two returns with the same account. You have to use two separate accounts.
Please keep in mind that we cannot see your tax returns or your screen. We don't know anything about you or your tax returns except what you write in your posts. Things that seem obvious to you may not be obvious to someone who has only a couple of brief messages to look at. When you say "on the 1040," it's not clear which 1040 you are talking about, since you are working on two separate tax returns.
As you are probably aware, when you file as married filing separately (MFS), if one of you uses itemized deductions the other must also use itemized deductions. You can't itemize on one return and use the standard deduction on the other return. In the Personal Info section of TurboTax for both returns, make sure you check the box that says either your spouse or you claim itemized deductions. See if checking that box resolves your Schedule A problem.
