I am the principal developer of the IMOD package, which uses MRC format. It now writes byte files as signed bytes by default, following a clarification of the MRC standard about 5 years that was formalized in a recent publication (Cheng et al. (2015) MRC2014: Extensions to the MRC format header for electron cryo-microscopy and tomography. J. Struct. Biol. 192, 146-150.). Users have recently reported that signed byte files do not read correctly (are not recognized as signed) when read into ImageJ through the scifio2 library or the regular import mechanism by drag and drop. They do read correctly when read in with the Bio-formats plugin.
It would be great if the files read correctly through whatever mechanism is used.