I accessed the retropie settings > misc > reicast options about adding a controler, and dimply ran that and told it to add the same PS3 pad, it asked for a few bindings which I set and others didn't (such as 'c' and 'z', no idea what those correspond to the dreamcast controller)

anyway now it works, no idea why it just stopped working. I did do a full retropie update yesterday though.