Married Filing Jointly vs Married Filing Seperate

We went through the TurboTAX questions as Married Filing Jointly and came to the end of the process where it checks to see which way would be the best way to file and we ended up having to pay in to both Federal and State close to $1000 combined.  So we went back to the beginning and changed our filing status to Married Filing Separately and the number jumped to receiving nearly $1800 back as a tax refund.  Common since would say this would be the better way to file this year and get a refund. This seems to good to be true or "easy" so we wondering what could be missing that is making such a drastic difference between each filing. Any advise would be greatly appreciated.