Hi Chel - I too am on clomid and yes I've had high progesterone and not been pregnant. Basically the progesterone level only tells you if you have O'd. If it's high then it means you have O'd a good quality egg or two. It does also give you a higher chance of falling pregnant, but it won't tell you if you are pregnant or not.
However, if you definately know that you O'd over two weeks ago and the BT came back negative and yet you still don't have AF then yes it is possible that you could be pregnant and it isn't showing up yet. I'd be going back for another BT if AF doesn't show.
Best of luck
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