I think I'm experiencing a bug, but perhaps there is a simple explanation and fix.
I have many initialization cells in my notebook (a few hundred). As of quite recently, they stopped all evaluating when I execute "Evaluate Initialization Cells". Some do, but some don't—I haven't yet detected any pattern. I can tell when they don't evaluate because, on top of the code not working correctly, I can still see In[•] next to the cell after "Evaluate Initialization Cells" is complete. But such cells are still grayed out and when I right-click their side panel, the "Initialization Cell" option is checked off.
Any ideas what could be going on? Is this definitely a bug? This might have begun recently after I had to force-quit Mathematica while it was stuck in a loop.