I can reproduce this every time. First I load all the layers. Then change layer color for any layer. Then try to load both NPTH and PT layers. Only PT layer shows up in the layer manager. All the holes appear correct. If at this point I go and try to load NPTH layer, it replaces PT layer in the layer manager and both plated and non plated holes are displayed. Some of the holes appear with wrong sizes. For example, I have a footprint with a ground pad and small thermal vias. Those show with the diameter of the board non-plated mounting holes (which are quite large). At this point trying to load any other hole layer doesn't change the hole layer being displayed.
Application: gerbview
Version: (2018-01-26 revision 0d532b43d)-makepkg, release build
Libraries:
wxWidgets 3.0.3
libcurl/7.54.1 OpenSSL/1.0.2l zlib/1.2.11 libssh2/1.8.0 nghttp2/1.23.1 librtmp/2.3
Platform: Windows 8 (build 9200), 64-bit edition, 64 bit, Little endian, wxMSW
Build Info:
wxWidgets: 3.0.3 (wchar_t,wx containers,compatible with 2.8)
Boost: 1.60.0
Curl: 7.54.1
Compiler: GCC 7.1.0 with C++ ABI 1011
Build settings:
USE_WX_GRAPHICS_CONTEXT=OFF
USE_WX_OVERLAY=OFF
KICAD_SCRIPTING=ON
KICAD_SCRIPTING_MODULES=ON
KICAD_SCRIPTING_WXPYTHON=ON
KICAD_SCRIPTING_ACTION_MENU=ON
BUILD_GITHUB_PLUGIN=ON
KICAD_USE_OCE=ON
KICAD_SPICE=ON
1. Add all the board layers
2. Change color of any layer
3. Add NPTH and PT hole layers