ArcGIS99. I use spatial analyst a lot and have never had any sort of data offset problem. Its unclear which Surface tool your first question refers to, though its not likely a matter of which tool as you report the same issue in your second question about a Conversion tool.
All I can think of is that you have spatial reference mismatches between some of your data--which I consider in general to be a problem to avoid/address before doing anything else;
or, that you were zoomed in to the data when you ran the tool and the processing extent was set to 'current display';
or perhaps that the 'offset' is just a single pixel around the edge of the raster in which there were some missing values that were ignored in the processing but which you're now interpreting as a shift in position;
or that when you converted the raster to polygon, you had the 'smoothing' option checked and that this 'moved' a few pixels when it smoother the new polygon boundary (such 'shifts of ~ 1/2 pixel width' are probably impossible to avoid when converting from raster to vector).
It would help if you provided images that illustrate the shift you're concerned about, and more info. about your input raster metadata...
