I called esri support to discuss this issue. They had no concrete fix but did recomend the following:
1. Please close all ArcGIS ArcObjects applications (ArcCatalog, ArcMap) when not in use and at the end of each day.
2. Verify within the SQL Server database table, sde.sde_process_information table that client connections are closed, or to review the time stamp listed for open connections.
3. It is highly recommended, though not required, to verify that all client connections are disconnected prior to executing an ArcSDE database compress. Any connection to the database will generate locks on the data and will thus prevent a full compress from being achieved.
4. Check the Firewall refresh / recycle rate, it may be possible that it could be conflicting with the ArcGIS Server map services refresh / recycle rate
5. It may be possible that the many scheduled tasks being completed each night are competing for server memory resources, please review and evaluate the concurrency of these tasks and consider alter the start times of these tasks so that they are more evenly spread out when using these server resources.
If additional errors continue to persist, please attempt to capture a Client Intercept trace, in hope that we can gather additional error logging.
