I’ve encountered an issue where, after working for a while ctrl + shift + click masks all other polygroups instead of isolating the on clicked on. Does anyone know what causes this?
I am new to Zbrush. However, as I am aware, this happens (“masking other poylgroups with ctrl + shift + click instead hiding them”) when you have transpose tool active instead of brush.
Hope this solves the issue, otherwise someone more experienced should probably reply 
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No need, you nailed it
This is a result of Shift-Ctrl-clicking while in Move mode as @horrorshowminis said. Please see the documentation on the Masking page for “Quick One Touch Masking of Polygroups”
http://docs.pixologic.com/user-guide/3d-modeling/modeling-basics/masking/