In general that's not a known issue. Pretty much everyone here at Netgate runs with a private domain entry for our company domain and things hum along as usual.
unbound can get cranky sometimes if it is trying to reach a specific upstream server and it doesn't respond. Keep an eye on Status > DNS Resolver entries when it works vs when it doesn't work. You can get the same output from the shell with:
: unbound-control -c /var/unbound/unbound.conf dump_infra
Odds are when it stops responding there is an entry in there for a server that has also stopped responding. Restarting unbound clears all that knowledge and forces it to try again. You could also try manually flushing things for that domain (or all domains) to see if that's sufficient to make it try again:
: unbound-control -c /var/unbound/unbound.conf flush_zone foo.com
There are some other similar commands to try listed in the docs:
https://docs.netgate.com/pfsense/en/latest/services/dns/resolver-cli.html