Hi,
It is hard to say what could be going wrong with your system. You can always get the newest versions of 488 from http://www.ni.com/support/gpib/versions.htm. If you look there, match your card to the vesion and you should be ok. I can tell you that your program should run the same in the newer version. We have maintained compatibility with the old API for backward compatability.
Hope this helps out.
Best Regards,
Aaron K.
Application Engineer
National Instruments