(I work for Fastmail). That sounds odd – have you contacted our support team so we can look into it? https://www.fastmail.com/support/
I didn't, but I'll do so now. I usually don't bother with support, because I forget that good companies like Fastmail actually have a competent support team.
Not OP, but I had to change the mail cache from all mail to recent, I think because it couldn't handle how much mail I had? It would often get stuck not syncing, and offline would be unreliable and showing a blank screen. Recent works fine, but it would be worthwhile folks testing more with all mail enabled, especially if they have larger inboxes.