Buliej...I am not an expert, but one reason could be that you were pregnant for a short time (ie your embryo implanted and kept growing for a while), and your body started producing the pregnancy hormone, and then your embryo stopped growing and you had a very early miscarriage. In those cases it can take a while for the hormone levels to go right back to zero. I know some of the other ladies here have had very low levels at their BT and been told that means the pregnancy is not viable, but it is classed as a miscarriage, or in some cases a missed miscarriage (if they have not started bleeding).
I am sure it is very frustrating for you when you want to move forward. I guess your FS wants to be sure all is right before you move on. Like I said, I'm not an expert on these things though.
As for your concerns about the doses of synarel etc, I honestly don't think it matters if you start sniffing a bit later into your period. I know when I was on the stim cycle, I actually started sniffing toward the end of my period (as my clinic has a set day they like you to start, and that happened to be towards the end of my period from memory). If you are worried though, ask your FS about that...perhaps ring her today to set your mind at ease. It's a bit different at different clinics it seems.
Good luck, let us know how you get on. I know it's stressful going through all this