From my own personal experiences with that same problem I am pretty confident that this problem will go away for you if you upgrade. At this point you are several major versions behind and there have been substantial improvements in the product.
I would also look into upgrading at least your polling system to Windows 2008 R2, you will get much better performance out of it as compared to Windows 2003.
We noticed where Customers started having SQL Connectivity issues where the SQL Server would drop our Connections, which in turn would stop polling. Starting in 10.0 and above Orion NPM now attempts to reestablish connection for all Services and reestablish Polling.