You mentioned the hormone being in pill form. So this probably doesn't apply, but I'll throw it out just in case.
With some hormones, they are applied as a gel to the skin. They can definitely transfer to another person for hours (in fact, some scientific literature has documented post-menopausal women transferring hormones to their pets, causing spayed female dogs to have periods). I've heard 4 hours for the amount of time between application of the hormone and when no transfer will take place. It's a well known problem and is documented in the insert with the gels.
Once again, this wouldn't apply to a pill. But I wanted to throw it out here for people to know about if they have a partner who uses a gel - it can cause serious health issues.
I would find a doctor though since it sounds like something is going on and it's worth checking out regardless of the cause. Depending on why you are on birth control pills, it may also be important to make sure they are functioning properly for you. As for your doctor, if your doctor is giving you weird vibes for being with your partner, I'd try to find another doctor. I personally will not see any medical professional that will judge me or my wife.
