Check the timeout setting on the server and in the client software.
Also, it is possible that blocking is causing the timeout?
You can run SQL Server Profiler trace to check performance.
Are you indexes deteriorated?
Make sure that dynamic tables are reindexed every night with FILLFACTOR 70.
Kalman Toth - Database, Data Warehouse & Business Intelligence Architect
Business Intelligence Workshop NYC SSAS, SSIS, SSRS - April 21-24: http://www.sqlusa.com/