Hi, I've had a similar thing happen to me. Soon it'll be 1 year since I started HRT, and shortly after switching to a cyclical regime I began noticing lower back pain. I'd never had back pain in my life, of any kind. I noticed it a lot more when lying down in bed to sleep, and I had nights where the pain would awaken me.
It's been 7 months of almost daily pain, sometimes more sometimes less, mostly at night in bed, but never so severe that I felt the need to go to a doctor. Just recently it's improved quite a bit, I've not increased or decreased my HRT dose, but I did start to take collagen, as well as an anti-inflammatory supplement called PEA (palmitoylethanolamide), so could any of these have something to do with it? Maybe it's to do with some adjusting process the body goes through when put on hormones, and eventually goes away, I don't know.
I think HRT has a lot of benefits and also for many women some side effects, could this be one of them? Maybe. I've also began to have episodes of headaches here and there, nothing important but it's caught my attention because I've never had that problem before, it's something completely new to me.
Another thing I noticed since HRT is worse leg circulation and spider veins and similar appearing or worsening, but that's a different subject.