There isn't enough from what you posted to really see what was going on. Is there a 'caused by' line in the debug log level after the LdapSyncException? The one posted in generic for any Sync failure, but ideally there should be a subexception. What I see here is the ldap sync failed with a specific provider.
The Sync is just to update user information (first name, last name, etc). The LDAP login process is independent of syncing.
Is there any cadence to the error state/emails? Like a time of day, or day of week? Is the service account used for this LDAP connection used in other applications?
In respect to the upgrade to 5.5.x generation, the LDAP code didn't change but the JRE Version did (to a release of 1.7, when vCD 5.1.x was JRE 1.6).
