And as the owner of a vagina (totally clean and un-infected LOL) I have seen what you have described a bazillion times... If I am regularly intimate with a man I tell him that I am either due for my period, just about done, so he doesnt have a heartattack if a bit of normal discharge ends up on his cock. My periods are sporadic so I never really know when this might occur. NEVER have I had a problem with any male I have been intimate with (and I am willing to wager that my number of partners is far less than yours, but it is certainly more than two! hehehehehhehee).
From what you describe, it could be an infection of some sort, or maybe she has undergone a procedure? Even a pelvic exam or pap test can bring on that kind of result; but the odour you describe is not typical I don't think. That's usually a sign of some sort of infection, or again she could be having post symptoms from some kind of procedure on her cervix.
You could ask her in a very kind way..maybe bring it up like you are concerned about what you saw and ask if she is ok? There's a good chance she wouldn't be offended if you handled it that way.
I thought she was retarded because she had a cone head. They didn't tell me that they sometimes come out that way. Wow, sometimes it seems like yesterday.