I'm having the same problem. Samba database connection refused after setting up users, groups, shares and then rebooting the machine. During Boot-up, a message appears on the screen that says something like "Zentyal is Setting up Core services" After reboot, the Zentyal-samba module is broken and can only be fixed by purge/reinstall (which throws away all the configuration you just did)
some modules reported error when saving changes . More information on the logs in /var/log/zentyal/
FATAL: Could not connect to samba LDAP server: connect: Connection refused
FATAL: Could not connect to samba LDAP server: connect: Connection refused at
FATAL: Could not connect to samba LDAP server: connect: Connection refused at /usr/share/perl5/EBox/Ldap.pm line 219
EBox::Ldap::safeConnect('EBox::Ldap=HASH(0x9484be8)') called at /usr/share/perl5/EBox/Ldap.pm line 173
EBox::Ldap::connection('EBox::Ldap=HASH(0x9484be8)') called at /usr/share/perl5/EBox/LDAPBase.pm line 99
EBox::LDAPBase::search('EBox::Ldap=HASH(0x9484be8)', 'HASH(0x7928a28)') called at /usr/share/perl5/EBox/Samba.pm line 1856
EBox::Samba::securityGroups('EBox::Samba=HASH(0x7d0cdf0)') called at /usr/share/perl5/EBox/Samba.pm line 1636
EBox::Samba::realGroups('EBox::Samba=HASH(0x7d0cdf0)') called at /usr/share/perl5/EBox/Samba/Model/SambaSharePermissions.pm line 84
EBox::Samba::Model::SambaSharePermissions::populateGroup at /usr/share/perl5/EBox/Samba/Types/Select.pm line 50
EBox::Samba::Types::Select::options('EBox::Samba::Types::Select=HASH(0x9707b98)') called at /usr/share/perl5/EBox/Types/Select.pm line 179
EBox::Types::Select::printableValue('EBox::Samba::Types::Select=HASH(0x9707b98)') called at /usr/share/perl5/EBox/Types/Union.pm line 384
EBox::Types::Union::AUTOLOAD('EBox::Types::Union=HASH(0x9707958)') called at /usr/share/perl5/EBox/Types/Union.pm line 252
EBox::Types::Union::printableValue('EBox::Types::Union=HASH(0x9707958)') called at /usr/share/perl5/EBox/Model/Row.pm line 547
EBox::Model::Row::printableValueByName('EBox::Model::Row=HASH(0x9707a48)', 'user_group') called at /usr/share/perl5/EBox/Samba/Model/SambaSharePermissions.pm line 144
EBox::Samba::Model::SambaSharePermissions::syncRows('EBox::Samba::Model::SambaSharePermissions=HASH(0x9615400)', 'ARRAY(0x9687858)') called at /usr/share/perl5/EBox/Model/DataTable.pm line 1461
eval {...} at /usr/share/perl5/EBox/Model/DataTable.pm line 1457
EBox::Model::DataTable::ids('EBox::Samba::Model::SambaSharePermissions=HASH(0x9615400)') called at /usr/share/perl5/EBox/Samba.pm line 3462
EBox::Samba::shares('EBox::Samba=HASH(0x7d0cdf0)') called at /usr/share/perl5/EBox/Samba.pm line 3248
EBox::Samba::writeSambaConfig('EBox::Samba=HASH(0x7d0cdf0)') called at /usr/share/perl5/EBox/Samba.pm line 804
EBox::Samba::_setConfInternal('EBox::Samba=HASH(0x7d0cdf0)', undef) called at /usr/share/perl5/EBox/Samba.pm line 780
EBox::Samba::_setConf('EBox::Samba=HASH(0x7d0cdf0)') called at /usr/share/perl5/EBox/Module/Base.pm line 995
EBox::Module::Base::_regenConfig('EBox::Samba=HASH(0x7d0cdf0)') called at /usr/share/perl5/EBox/Module/Service.pm line 972
EBox::Module::Service::_regenConfig('EBox::Samba=HASH(0x7d0cdf0)') called at /usr/share/perl5/EBox/Samba.pm line 761
EBox::Samba::_regenConfig('EBox::Samba=HASH(0x7d0cdf0)') called at /usr/share/perl5/EBox/Module/Base.pm line 234
eval {...} at /usr/share/perl5/EBox/Module/Base.pm line 233
EBox::Module::Base::save('EBox::Samba=HASH(0x7d0cdf0)') called at /usr/share/perl5/EBox/GlobalImpl.pm line 651
eval {...} at /usr/share/perl5/EBox/GlobalImpl.pm line 650
EBox::GlobalImpl::saveAllModules('EBox::GlobalImpl=HASH(0x48ee178)', 'progress', 'EBox::ProgressIndicator=HASH(0x230b8f0)') called at /usr/share/perl5/EBox/Global.pm line 95
EBox::Global::AUTOLOAD('EBox::Global=HASH(0x48edba8)', 'progress', 'EBox::ProgressIndicator=HASH(0x230b8f0)') called at /usr/share/zentyal/global-action line 32 eval {...} at /usr/share/zentyal/global-action line 30