OK. It would be useful for you to mention that at the start, although I don't know why it doesn't number them sequentially.
Edit: Just tried this with a plain PCB which isn't in a project and has no schematic. None of the components had the ? number (that is, they were already C1, C2, etc. I chose ascending x then ascending y, then all the various combinations and even 'use board position'. Every time the component designators were changed appropriately.
You might try click a component, then right click and select 'same as' using only 'component' as the match. That will select all components. Then run the re-annotate and see if that helps. If not then your board is borked or your designators aren't actual designators, or something similar.