JIRA does not currently support connecting to load-balanced AD servers.

http://confluence.atlassian.com/display/JIRA/User+Management+Limitations+and+Recommendations
About half-way down:

"#2) Synchronising between AD servers is not supported. Microsoft Active Directory does not replicate the uSNChanged attribute across instances. For that reason, we do not support connecting to different AD servers for synchronisation."

Many companies have a single DNS entry (mydomain.mycompany.com) that points to a load balancer that directs traffic to one of many directory servers. (Or, some companies might use DNS round robin.) However, neither the use of DNS round robin nor use of an actual load balancer is supported by JIRA – both approaches to load balancing direct traffic to different servers, which would violate limitation #2 above.
Currently, JIRA only supports connecting to a single directory server, not different (load-balanced) servers.