As a "special feature", Bruker's CompassXport tool filters out all the zero-intensity points to produce smaller files. I think, this is a very bad "feature" and I'm happy that a simple trick can be applied to "disable" it. In mMass's preferences, select the "mzML" data format in CompassXport section. It might take little longer to convert and load the data (especially for high resolution spectra) but the result is much "real". For both mzXML and mzData formats, all the zero-intensity points will be removed.