We currently use IS 6.0.1 + TN + SAP Adapter 4.6 SP5 with JCo 2.0.10.
When we migrate to IS 6.5 we will use Windows 2003, but not yet sure whether to stay with SAP Adapter 4.6 or use SAP Adapter 6.5.
One issue is Java Connector and Windows version. SAP note 549268 says that JCo 2.0.x is only certified for Windows 2000 (whereas JCo 2.1.x is also supported for Windows 2003).
Is anybody running SAP Adapter 4.6 on Windows 2003? What JCo version are you using? (you can view JayCo version from About page on SAP Adapter gui).