The dick in question was small and I had disabled forced transformation, so those aren't the reasonsThere's no such thing as "no reason" with the transformation system.
Gender identity is only one part of what influences the transformation system.
Since you went from trans back to male body, I'd say you probably gave your MC a large/the largest penis size. Whilst that's great for natural dominance gain, it works against female/feminine transformations. Clothing as well also factors in.
The dreams when sleeping also convey information hinting at transformation paths. You should have seen it mentioning your MC feeling masculine.
To avoid Forced Transformation, restart and select that you've played the game before.
One of the Saya dreams will present the option to disable Forced Transformation and allow you to either avoid the transformation dream when it happens, or an option on the sidebar to disable it entirely.
There weren't dreams about becoming more masculine when the body type changed
I don't know whether I'm a weird edge case, I'd have thought this a more common issue as it's happened three times on separate playthroughs and game versions