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After much troubleshooting. We found that the oq.connection_reg and oq.app_lock indexes were extremely large (100000 pages) and highly fragmented (99%+). The users were timing out on getting connections with the smart client because of the slow returns on the connection reg index. Restarting the IIS Server did not help and stopping all services did not help.
DBA rebuilt both the oq.connection_reg and oq.app_lock reg. We then restarted the IIS Server, launched the server monitor and then restarted the application server. Once it was of status OK we then successfully launched a smart client connection. After which we launched the remaining 3 services (1 ODC, 1 Action Scheduler/job service provider and 1 Job service provider.DBA expert recommended daily rebuild of the two indexes.
Users that perform a large amount of dataloading regularly have a greater need for regular maintenance of these indexes.