Arc 9.x converts all rasters to grids before it runs its tools. I have seen where the new direct read/write fails to work on some input formats correctly. You should definitely log a support incident if you can reproduce the issue.
What is your input data type? If it isn't a grid, then try converting it to Esri Grid format with copy raster and see if the tool will run correctly on the grid format data file.
One thing about grids is they always have a valid raster table and stats, they are built with the grid is created -- not necessarily true with other raster data types, so just running Build Raster Attribute Table or running stats on the raster may fix your problem.