We've had several NI-VISA releases since 2.5 - so I suggest you upgrade to NI-VISA 3.0. While there isn't anything specific to your type of problem in the Linux version of our readme.txt, I know we've made a number of other fixes.
While the most recent release is NI-VISA 3.1, I still recommend you upgrade only to 3.0.
This is because NI-VISA 3.1 requires the new NI-488.2 release for GPIB-ENET to be installed (even though you aren't using that product). This is due to some internal rearchitectures, and the PCI-GPIB product is not released. If you do want to go with NI-VISA 3.1, the new NI-488.2 release for GPIB-ENET on Linux will still work with the PCI-GPIB beta driver that you have installed.
Dan Mondrik
National Instruments