Are you using IPv6?

IPV6 is enabled but all names are resolved by hosts in IPV4 format.
Do you whant I try to disable IPV6 at network level?

I disabled all the ipv6 network stack but the problem still happens.
I have also some segfault errors:

[502730.916920] sogod[30562]: segfault at 7fd084e546b0 ip 00007fd084cf6348 sp 00007fff60efc6c0 error 7 in libgnustep-base.so.1.24.7[7fd084b7d000+4c0000]
[595715.257991] sogod[9277]: segfault at 0 ip 00007f5dffcb8264 sp 00007ffe74db1610 error 4 in libc-2.23.so[7f5dffc4b000+1c0000]

Is there a Firewall between your SOGo Server and your LDAP/database?
Perhaps that kills connections in between.

Do your LDAP and database have limitations on how many connections can be made?
We had problems because of that every time "sogo-tool backup" was running, as it generates one connection per user.

Like I said before, the problem is random. All day long the sogo boxes can work and randommly they lost connections. In advance, if I enter in the system shell, I see sogo errors but I can use the remote ldap and mysql services using telnet and openssl and mysql client.

We have two sogo boxes. One is in LAN and connects to a Ldap server in LAN and to a mysql database locally (installed in box). The other one is in a DMZ, and connects to the LAN ldap server and to the LAN sogo box.

Do you think that the default limits of MySQL and Windows Active Directory can be reached? I can try to verify at the next error if the limits are reached but as I wrote before, when sogo can't connect locally to it's database, i can via mysql client.

In our case the problem was that SOGo eats OS error messages in case of network errors.

So the "you ran out of file descriptors" error gets translated into completely bogus "Can't contact LDAP server"