Can you provide your Prodigy version? Ideally, if you can provide prodigy stats.
I think you may be running into this issue:
I think this was transformers related, but I'll need to check with colleagues.
Also - just curious, can you run spacy debug config? This helps us rule out if there's just an error with your config. Even better, if you could provide the config too, but if not, at least running debug config.