If this is something that has been deployed for a while, prehaps a crashed index. Look for an error messages relating to the database in .../reporter/log/server_err.log. If you see something like "Table 'xxxx' is marked as crashed" try repairing it with myisam check. Otherwise I would need to see the error from the log.
No crashed tables in server.log the first error messages are these
2012-04-10 03:17:17,383 ERROR [securecomputing.smartfilter.server.project.reportdbbuilder.tasks.DatabaseMaint enanceTask] Reporting database is not available.
2012-04-10 03:17:21,460 ERROR [securecomputing.smartfilter.server.project.services.updateDirectory.UpdateDire ctoryTask] FAIL_REPORTING_DB_NOT_AVAILABLE
2012-04-10 03:17:44,627 ERROR [securecomputing.smartfilter.reportengine.drilldown.DrilldownReportServer] reporting database is currently not available, state=use trI18n(I18n) - ReportDbStateEnum
2012-04-10 03:17:44,642 ERROR [securecomputing.smartfilter.reportengine.drilldown.output.buildxml.XmlDocBuild er] Aborting
Can't see anything indicationg why it can't connect
It is safe to run myisamcheck on all of the MYI files even if they are not crashed. I can't think of any other reason why the DB test gave you the schema version number, but does not stay connected.
You could also try restarting both the Web Reporter and Internal DB services. I recommend you stop them, then check the task manager before starting them again. Web Reporter is the java.exe process owned by the SYSTEM account, the internal database would be mysqld.exe.
Server rebooted on 8th April at 3am during database maintenance could this have left the database in a bad state, is there any integrity checking I can do ? can I run the rebuild indexes manually ?
2012-04-08 03:01:19,835 ERROR [securecomputing.smartfilter.server.project.reportdbbuilder.tasks.DatabaseMaint enanceTask] Failed to complete rebuild indexes maintenance
com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
Yes, it's very plausable. Running myisamcheck as previously mentioned is a good place to start.
Ran against all tables overnight and Reporter started ok this morning
Would a windows 64bit system give a noticeable performance benefit ?
Performance in what regards? Log parsing? Running reports? Maintenance?
What specific performance issues are you noticing?