Hi,
You should use whatever gender marker Social Security has you down as. That is what these are checked against. If you have mixed documents (DL is female, SS is male as an example), you would need to let your background investigator know that there will be inconsistencies in your documents.
I've had a few of these done. It's always fine as long as you inform them ahead of time that things are messy. They may even advise you on which to use.