Similar thing happend to me on EE as well. For my first IVF, I took it for 6 days prior to AF, went in for CD 3 b/w and my E2 was only 12!! They said this was definitely the EE at work, and I had 7 follicles under 8mm and for the first time ever, no leads. They told me to keep taking it before starting stims, and i did. (I was taking it every day). Even after I started stims (I think on CD 5 or 6?), my E2 was hardly rising...so they said i was oversupressed and i opted to go every other day on EE. As soon I took it every other day, my E2 started rising and follicles grew. So, I think for som people it can really oversupress...I eventually stimmed for 12 days. The 2nd time I took EE in the LP to prep for IVF, I took it every other day, and on CD3 my E2 was 25 so I wasn't nearly as supressed. i also told them there was no way I was taking it again while doing the stims, and they were okay with it. That time I only stimmed for 6-7 days.
i was going to do IVF this cycle so took EE again last cycle (we ended up NOT doing IVF this cycle though), this time every day again until AF...and I think it oversuprssed me again because I still haven't ovulated and I am on CD30! (i have a big follicle though ready to go now, so eventually things got going on their own)
So, don't worry too much! I think you are probably oversupressed, once you start the stims you should be fine. And maybe ask hem if you can do EE every other day (or not at all?). If you do a search you can find my frantic post about this back in March (around beginning to mid March) and see the responses about oversupression (I can't post links on this computer for some reason).
BTW, I posted to you below, not sure if you saw it, but I was curious about how your immune treatments are going and wishing you luck!