Microsoft recently published a new KB article that contains information about the logging improvements that have been made in the System Center Operations Manager DataWarehouse where SQL time-out exceptions are concerned. This information should help you troubleshoot SQL time-out scenarios.
For all the details please see the following:
KB3029227 - How to troubleshoot SQL time-outs in Data Warehouse after you install System Center Operations Manager R2 Update Rollup 5 (http://support.microsoft.com/kb/3029227)