It might be helpful to see the full command you used and maybe a little information about the datasets. You might run into a problem like this if you are also going from a higher resolution to a lower resolution. You can see some more discussion of this issue in 3dfractionize's help. The -clip option helps control how voxel values are set in 3dfractionize. For 3dWarp, you could use a linear interpolation instead and then use 3dcalc to turn the non-zero voxels into an integer.