Anyone (married) tried running Turbo Tax "Married filing seperately"?

I used the free version of Turbo-tax as our finances are pretty straightforward... we both had 1 job (W-2) all year, we rent so no deductions there, we have 1 daughter (2 years old) and pay daycare. When I plugged everything in with Married Filing Jointly we owe $939. Just to see what the difference would be I tried filing us separately as Married filing separately. I selected the option that we lived together and we lost the credit for Child Care Expenses, BUT it turned out with me owing $741 and her receiving a REFUND of $1308. I have always been told that filing jointly saves the most on deductions... but not the case here. What gives? Should I file separately? I think my wife falls in a different bracket as she earned less than $35k. Any advice would be appreciated as this goes against the conventional wisdom I have been told with taxes. I'm pretty sure I entered everything accurately.