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I'm not sure if this is helpful or not, but when I was on the pill, I would start on a Sunday and finish them on a Saturday..my period didn't usually start until the following Tuesday...so 3 days after I finished the pill.
I would take the last real pill on Saturday and it was common for my period not to start until Tuesday or Wed. I think your dr is jumping to conclusions and should not be saying things like that. The pill will affect your cycle. hang in there. I think it will come soon.
I think it just takes a little while for the birth control to get completely out of your system. I took birth control to regulate my period, because I would have it all the time. And it would take a few days from my last actual pill before it would actually start. And then it was the same thing at the end of the "green" placebo pills..I would take the last one and then it would take a couple days for my period to stop.