Upgrading from different versions of LabVIEW shouldn't be a problem; I would suspect different versions of NI-DAQ first. Make sure you use the Measurement and Automation Explorer (MAX) to configure your card.
To see if it's a driver update issue, when you use the LabVIEW 6 installation CD, choose custom install and don't upgrade your drivers. You may have to browse into your LabVIEW 5 directory and use copies of the VIs from there.