There are a few things I can think of that can cause this:
- I know you said your flour is fresh, but using your finger, taste a tiny bit of the flour raw. If it's at all bitter, the flour is not fresh and going/have gone rancid.
- Are you making a sourdough type bread with regular yeast as a start? I have had some batches of overactive yeast flavor my bread with a beerlike flavor that's a bit bitter. I usually ease up on the yeast in that case.
- Are you soaking your flour and if so, are you using whey? If so, taste your whey. I noticed that some batches of my whey turn out a bit bitter while some have not much taste at all. I make my whey from kefir and noticed that the kefir brewing temperature and conditions will affect the flavor of my whey.