I'm using 10 too, but I had the same problem in 9.3.
I contacted ESRI support center, and I got a very helpul and easy workaround. The fix was from the Environment Settings > Processing extent, where you basicaly choose the original raster for extent and snap raster. I didn't have a problem with the values in the shapefile being output with a different value in the raster. My output had 5 values: the original 4 from the shapefile plus 255, so they didn't range from 1 to 255. And the 255 value was outside the extent of the shapefile. But got it fixed. However, I think I did encounter your problem previously, if I understood you well, so what I did was I saved the raster as an .img, and exported it as an untiled tif using Imagine and the output had the same number of values as the shapefile (although I think they got shuffled).