We teach a large GIS class in the fall, and we have see this problem, and many general raster problems, in the class for years using many different versions of ArcGIS. Currently, we are running ArcGIS 10.1 on Windows 7. The students are running the tools and saving outputs to a networked server where they have an account. An example of this problem is a simple raster multiplication. I have a LULC. I want to subset this to a smaller area. I have a mask of the smaller area composed of 1's where I want to keep values and NODATA in the background. (the mask is a single USGS quad sheet, the LULC is for an entire watershed). I use raster calculator to multiply the mask * LULC. The output is subset to the extent of the mask, but it is assigned a value of zero for all pixels where the mask has values of 1.
I can get the subset to work with the CON tool, but not the raster calculator. It also fails when I put all the data on the local C: drive and set the scratch space to the C drive as well. Sometimes removing the network from the situation has solved these raster problems, but not this one. We have asked ESRI about this problem a number of times, but so far no solution. The exact nature varies a bit from on version of ArcGIS to the next, but always these types of raster function errors.