@Adam_B have you tried reaching out to SmartThings support? It seems they are a bit swamped right now, so they might take a while to respond, but it’s worth logging the issue with them.
Also, @obycode and others have had similar issues with their V1 Minimotes with Hub V2. It looks like Brice got his to work after updating the firmware on his remote, but it sounds like you’ve already done that. (Other people are seeing erratic pairing issues with their remotes as well, so it’s probably best to report it to support)