So I told him she made me uncomfortable and he has kind of played on that ever since.
That's what they do. To begin with they're the most charming, fun, caring, charismatic, 'just get you' guy and once you're hooked they start with very subtle, hardly noticeable, digs. So small you think you're imagining it - 'my lovely whoever wouldn't have meant that, it must be me'.
So you carry on trusting them, carry on sharing your innermost thoughts with them - tiny dig, no it can't be, fun times, tiny dig, tiny doubts, more fun times, you share some more with them, this carries on for however long until BOOM they slap you in the face with that deepest darkest secret that you shared with them. Just as soon as your heart starts slowing down after that shock there's another one, then he's all sweetness and light again and can't understand why you're not all sweetness and light back, you really are hard work, you're lucky he puts up with your moods.
He doesn't like you, newstart, he's just using you (and the other one) to boost his shitty little ego.
I hope you manage to make a clean break from him and become yourself again very soon 