Crystal reports don't run well after Windows Update installs .net 2.0 and .net 3.5

 I have a web reporting application build using VS2003 and Crystal ver 9.5.
Everything was working fine until the infrastructure team run the windows 2003 server WINDOWS UPDATE where the new .net 2.0 & .net 3.5 got installed.
I started to get CrystalDecisions.CrystalReports.Engine.InternalException: Error in File:crreport5.rpt -The request could not be submittted for background processing.
After I restart IIS , the reports start working again but they stop after a while and I have to restart again ...
Please, advise.