I believe strongly that our bodies and muscles adapt over time to a wide range of positions.
My Rivendell fits me pretty well, but like many women I experience some difficulties due to the proportions of having a bike tall enough for my legs but consequently a bit too long in the top tube, causing reach and weight balance issues for me. I have ridden this bike for a year and a half and over 5,000 miles now. Over this time, it has amazed me how my body has attempted to change and compensate for the various tweaks I have done to the bike in the pursuit of better fit. Things that made me sore at first didn't bother me at all several months later. Other things that didn't bother me months ago bother me now. The body is not static, and it is constantly trying to accommodate to perform what we ask it to do.

I think there are similarities in exercising. When I go through a period of lots of bike riding and little fitness walking, then when i start walking a lot I get terribly sore for the first few times- my lower back, my hip joints, leg muscles, shoulders...all get quite sore for days until they get used to the walking again.
The very same thing then happens in reverse- when I go back to my bike after mostly walking for weeks, I'll get very sore until my body adapts again.
(obviously I have now learned that it's best to keep up with both activities!)
On the extreme end- when I first decided to change my life by starting to fitness walk after many years of no exercise at all, I walked only a mile or so every day and yet I was terribly sore and hurting from head to toe....and it took about 4 weeks of daily walking for the soreness to finally fade away completely. All that seems silly to me now, but it shows that even doing something good for the body at a moderate level can hurt if the body is not used to the new positions and activity.

Luna Cycles, a women-specific builder, is making me a new custom bike- made to my exact measurements. It should be ready in the Spring.
There is no doubt in my mind that the new bike will fit me way better. But- there is also no doubt in my mind that when I first start riding my better-fitting Luna bike, I will likely experience a lot of soreness for days or weeks as my body is suddenly thrown into a hundred little changes in positions that are all subtly different from the old learned positions. I fully expect the new bike to feel weird and maybe even feel "wrong" at first because my body is so used to the Rivendell. Knowing this, I am quite prepared to give my body the time it needs to change in a gazillion tiny ways.

In my opinion, soreness is perfectly normal any time we make even small body position changes- even changes for the better. And soreness can last for many days while our bodies adapt. It doesn't necessarily mean that there is something wrong- just that there is something new.