OK, so I'm using Bind now and is working great with the domains, sometimes the subdomains are not reachable. I don't know where to look for errors (and probably I would understand much of them :(). I'm currently using my Bind server as nameserver (I've set up one for all domains) and the free service provided by dnsever.com. I've made all the settings on the registrar's page and there I've added my 2 ns plus 2 ns from dnsever.com. I've also enabled the "DNS domain enabled?" in every subdomain and haven't changed anything in their bind configuration.
I really don't know what is causing the subdomains to disappear like that, especially since it doesn't happen all the time. Should I give up the free dnsever.com service or am I doing something wrong with my server?!
I'm looking for errors in /var/log/messages but there's nothing pointing to subdomains and the "named" errors are showing other ns, like for example discuz : "Nov 22 05:07:25 L095 named: FORMERR resolving 'www.discuz.net/AAAA/IN': 184.108.40.206#53"