Interesting... Did you try a smaller cellsize just to test to see if you get more records? Did you try Steve's suggestion to check and repair geometry? You could also try converting the feature class into another feature class before attempting to convert to raster. The issue isn't with the zonal tool at this point. It's either some bad data or something with the conversion tool. However, the conversion to raster has pretty much always worked for me in 10.1. Do you have sp1 installed? If not, try installing it and test again.
Can you creat a support ticket?