Check the output of
3dBrickStat -min -max mydset
3dBrickStat -min -max -slow mydset
Also what does 3dinfo report on the min and max. If these are different from the last "slow" command, you may want to run
3drefit -redo_bstat mydset
With the same dataset as the underlay, you can also right-click on the image viewer and see the "bg" value for the voxel value. That will remove the effect of interpolating the overlay dataset to the underlay. 3dmaskdump can be used to get the value at the command line.