Yes, I understand what you are saying.
The problem is, that the IRS WILL assume you both benefited from the return, and any additional taxes or any refunds would be joint responsibility unless you show that it is not your fault or otherwise your responsibility.
So you have only two options to make sure this does not happen.
Option one. File for an injured spouse determination, for 2006, even though there is no refund, and include a copy of the divorce decree front cover, signature page, and pages mentioning the tax treatment as evidence. OR
Include a letter with your manually filed 2007 return, with cover letter explaining the circumstances in regard to the 2006 return, and include the same evidence.
Your SSN is on the joint return, and the IRS will cross reference the SSN's. So they will know that you filed joint last year and this debt hangs over, and your current year return will then be at risk.