I asked this very same question and it appears that your body is trying to get rid of the bacteria in the vagina which is what I was told. Hope this cured up for your.
Yes, the difference is the medication in pill form. You get a more consistant dose instead of the one big dollop each time you use the gel form. Talk to a pharmacist though, they either know off the top off their head or will look it up. They are more educated in how the meds actually work in the body & their affects on the body.
I am sure someone will be chiming in that has had this experience. I haven't, but did want to recommend you call your Dr. When pregnant, it is always best to run any concern past your OB. Good luck to you.