In NI-488.2 help (under Start, Programs, NI-488.2, NI-488.2 Help), see the topic "Automatic Serial Polling Overview". VISA leave the autopolling setting the same as you left it in the MAX properties of the GPIB board when you open a instrument handle on that board (so if Autopolling is turned on in MAX, it'll be on when you open a VISA session too). VISA will change the autopolling setting to TRUE if you do something that makes it need Autopolling, such as doing an viWaitOnEvent for the RQS event, or a viNotify for the RQS event.
You can handle the issue a few different ways. If you never use the RQS event, then you can disable Autopolling in MAX and it'll never queue serial poll responses. If you sometimes use autopolling, you can clear your instrument by doing a CLS and then doing viReadSTB's until you get a non-positive response to the function (bit 6 isn't set). This means that you have cleared out the autopoll queue and any future serial polls you request actually generate a "true" serial poll on the bus rather than pulling it from the queue.
Hope this helps. Autopolling is tricky but necessary for certain functionality.
Scott B.
GPIB SW
National Instruments