This problem has been present since the CarpetHDF5 plugin for VisIt became part of the standard VisIt distribution and it is still present in the current version of VisIt (2.8).
When Pseudocolor is used in log scale and Centering is set to Original or Nodal, not all the values of the plotted quantity are shown (in particular lower values are not plotted at all). This does not happen if one sets Centering to Zonal, which instead shows the correct values.
I have attached a couple of images showing the problem (they show hydrobase::rho for a BNS run).
I do not know what may be causing it, but it may cause serious errors when analyzing data with VisIt (since one may miss some of the information on the low value regions).