I found out how to duplicate the bug reliably with my settings as they are.
I'm sorta guessing what the Diff Pair settings should be. My board has both imperial and metric parts. The imperial parts are placed on an imperial grid, and the metric parts were placed on a metric grid. The board has fill zones surrounding the board on the imperial grid.
Set the above settings.
Save the file.
I've duplicated this at least 5 times in a row.
Version: (2017-09-08 revision 19ad350c1)-makepkg, release build
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 7 (build 7601, Service Pack 1), 64-bit edition, 64 bit, Little endian, wxMSW
wxWidgets: 3.0.3 (wchar_t,wx containers,compatible with 2.8)
Compiler: GCC 7.1.0 with C++ ABI 1011
ON EDIT: It happens when I press the B key to rebuild the zones, save, exit, and re-open.