Are the phones that are having problems behind their own NAT firewall?
It may be a NAT timing issue. Try changing the quality frequency in the Extension Settings for the affected extensions (the ones that cannot be called) to 30 seconds instead of the default 60 seconds.
Alternatively, it could be a registration timeout issue as well. Configure the phones to re-register more often, i.e. every 30-60 seconds instead of every 5 to 10 minutes.