Sites late online after server reboot

On my server, almost all my sites are extremely late online after server reboot, or up to half an hour or so.

I didn't have this problem before until I noticed this last winter. I reboot the server when it has been online for 2-3 months.

This is Apache 2.4 web server on a VPS.

 

I'm not sure if that is reason as the server is up and running, and all cPanel control panels and one site online, but just several sites down for about half an hour.

 

I didn't see anything in the apache error log at that time so I rebooted the server again to see if I might find something new.

1. Apache server was up and running within a minute
2. One site was online within at least two minutes, exactly as happened last time with the same site
3. But the other two sites were not online, exactly as happened last time
4. One of these two was online after about 20 minutes
5. The other one online after more then 30 minutes

Within few minutes from reboot these were entries in Apache server status page:

The client IP's in front of the server IP are all mine when one site was online but the other one's not.

xx.2x9.xx8.2xx
xx.2x9.xx8.2xx xx.1xx.xx6.x:80 NULL
xx.2x9.xx8.2xx
xx.2x9.xx8.2xx xx.1xx.xx6.x:80 NULL

Apache error log:

Code:

[Mon Aug 11 18:42:03.443517 2014] [mpm_prefork:notice] [pid 1245] AH00169: caught SIGTERM, shutting down
[Mon Aug 11 18:42:32.001932 2014] [ssl:warn] [pid 1247] AH01906: server.xxxxxxx.com:443:0 server certificate is a CA certificate (BasicConstraints: CA == TRUE !?)
[Mon Aug 11 18:42:32.002455 2014] [suexec:notice] [pid 1247] AH01232: suEXEC mechanism enabled (wrapper: /usr/local/apache/bin/suexec)
[Mon Aug 11 18:42:32.002523 2014] [:notice] [pid 1247] ModSecurity for Apache/2.8.0 (www.modsecurity.org/ ModSecurity: Open Source Web Application Firewall) configured.
[Mon Aug 11 18:42:32.002537 2014] [:notice] [pid 1247] ModSecurity: APR compiled version="1.5.1"; loaded version="1.5.1"
[Mon Aug 11 18:42:32.002546 2014] [:notice] [pid 1247] ModSecurity: PCRE compiled version="8.35 "; loaded version="8.35 2014-04-04"
[Mon Aug 11 18:42:32.002553 2014] [:notice] [pid 1247] ModSecurity: LUA compiled version="Lua 5.1"
[Mon Aug 11 18:42:32.002559 2014] [:notice] [pid 1247] ModSecurity: LIBXML compiled version="2.9.1"
[Mon Aug 11 18:42:32.002566 2014] [:notice] [pid 1247] Status engine is currently disabled, enable it by set SecStatusEngine to On.
[Mon Aug 11 18:42:33.001166 2014] [ssl:warn] [pid 1263] AH01906: server.xxxxxxx.com:443:0 server certificate is a CA certificate (BasicConstraints: CA == TRUE !?)
[Mon Aug 11 18:42:33.002798 2014] [:notice] [pid 1263] mod_ruid2/0.9.8 enabled
[Mon Aug 11 18:42:33.018560 2014] [mpm_prefork:notice] [pid 1263] AH00163: Apache/2.4.10 (Unix) OpenSSL/1.0.1e-fips mod_bwlimited/1.4 configured -- resuming normal operations
[Mon Aug 11 18:42:33.018603 2014] [core:notice] [pid 1263] AH00094: Command line: '/usr/local/apache/bin/httpd -D SSL'