Thank you for your response, I appreciate that.
I agree with what you wrote there so I wondered if that box was only meant for those who meet the exception to file jointly and be claimed as a dependent. I dug into f1040 instructions for that particular section, lo and behold, those boxes in the "standard deduction" section on 1040 relating to spouse should only be checked if the return is being filed jointly.
For anyone else married filing separately and running into Reject Code F1040-461: If your spouse can be claimed as a dependent on their MFS return, please uncheck the "spouse can be claimed as a dependent" box on your return. Even if it is true, this statement is not meant to be answered by MFS taxpayers. It says in the 1040 instructions that this box should only be checked if the return is MFJ (in cases under the exception mentioned by JohnW152 above). I unchecked the box and re-efiled, return was accepted.
