1. Have you cleared all of the gating discoveries in the handbook? Those are things you know you need to know more about.
2. If you find research fragments, are they blank, or are you discovering things? You have to find fragments at some point to continue.
3. Have you, in fact, crafted at least 1 of each of the things you can now craft? Or are you trying to craft 64 of one item, expecting that the total crafting is what counts (as opposed to number of different things crafted)
Q: Reika: Can you clarify what the fragments are supposed to represent? If its just "what you figure out by wandering around, looking, and exploring", that doesn't really fit the issue of them being mostly in your structures, and occasionally in dungeons / strongholds. "Notes made by others before" does make sense, but then, how did they do the research to write those notes, and why can't you do that research yourself?