pfSense

For better replication this is what happening:
IP_Alias_10 IP_Alias_6, IP_Alias_2, IP_Alias_1, IP_Alias_3, IP_Alias_4
IP_Alias_1 fqdn1.server.com, 1.1.1.1
IP_Alias_2 fqdn2.server.com, 1.1.1.2
IP_Alias_3 fqdn3.server.com, 1.1.1.3
IP_Alias_4 fqdn4.server.com, 1.1.1.4
IP_Alias_5 1.1.1.5

After pfSense boot this is working properly. After altering any of aliases (changing ip) iP_Alias_5 is missing in pfSense tables completely.

And IP_Alias_10 contains only IP address from IP_Alias_5

@Tomas - your description of IP_Alias_10 includes IP_Alias_6
But IP_Alias_6 is not mentioned anywhere else.
Is there a typo? Should IP_Alias_10 include IP_Alias_5?

Yeah, sorry this is typo, correct one is:
IP_Alias_10 IP_Alias_5, IP_Alias_2, IP_Alias_1, IP_Alias_3, IP_Alias_4

Update, it is not working even with filterdns.fixed, after some time, if I reload some firewall rules tables are mismatch...

In the log there is correctly: filterdns: adding entry 1.1.1.1 to table IP_Alias_1 on host fqdn1.server.com
But in table this address is not present.

Another observation, after some time (30min-60min) its recover from badly filled tables and are filled with proper IPs.
But in meantime traffic is blocked because ste of tables is not aligned with what was defined in GUI.