My recommendation is to move to all 32-bit if possible. The 16-bit version of NI-VISA is no longer supported. I think the latest version is 1.1, from 1997. So if you encounter any problems, you're pretty much on your own.
Now with the disclaimer out of the way, here's what you would need to do. The NI-VXI driver must be 16-bit, on Windows 9x, and you must install the NI-VXI thunking/compatibility layer version 1.1:
ftp://ftp.ni.com/support/vxi/drivers/Archive/atmxi/win95_98_thnkr/1.1/
You must install NI-VISA for Windows 3x version 1.1:
ftp://ftp.ni.com/support/visa/drivers/Obsolete_drivers/win16/1.1/
You can install any 32-bit NI-VISA for Windows (9x) version that you want. I recommend the latest version, since we always have bug fixes, but we
haven't tested against the thunking layer in the last couple of releases.
If what is on your current system is a 32-bit-native NI-VXI driver, then 16-bit VXI applications just will not work. The Windows architecture makes this difficult if not impossible. NI does not support this combination.
Good luck,
Dan Mondrik
Senior Software Engineer, NI-VISA
National Instruments