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I at least found what was causing CMake to go to the wrong version, though I still don't understand why. The 3rd party software is the Universal Robots SDK and during install it had added /opt/urtool-3.0/bin to my PATH. Removing it from PATH allows CMake to find the correct Boost installation.
If anyone knows how the PATH variable can affect CMake, I'd be interested to know as I couldn't find any reference to it in CMake documentation. I've listed the contents of the urtool-3.0/bin folder below and I don't see how any of them could affect it either.
[I] ~> ls -la /opt/urtool-3.0/bin/
total 14400
drwxr-xr-x 2 root root 4096 Sep 8 22:14 ./
drwxr-xr-x 13 root root 4096 Sep 8 22:14 ../
-rwxr-xr-x 1 root root 198404 Jun 6 2016 curl*
-rwxr-xr-x 1 root root 5073 Jun 6 2016 curl-config*
-rwxr-xr-x 1 root root 573920 Jun 6 2016 i686-unknown-linux-gnu-addr2line*
-rwxr-xr-x 1 root root 540928 Jun 6 2016 i686-unknown-linux-gnu-ar*
-rwxr-xr-x 1 root root 780256 Jun 6 2016 i686-unknown-linux-gnu-as*
-rwxr-xr-x 2 root root 132032 Jun 6 2016 i686-unknown-linux-gnu-c++*
-rwxr-xr-x 1 root root 570080 Jun 6 2016 i686-unknown-linux-gnu-c++filt*
-rwxr-xr-x 1 root root 130688 Jun 6 2016 i686-unknown-linux-gnu-cpp*
-rwxr-xr-x 2 root root 132032 Jun 6 2016 i686-unknown-linux-gnu-g++*
-rwxr-xr-x 2 root root 129504 Jun 6 2016 i686-unknown-linux-gnu-gcc*
-rwxr-xr-x 2 root root 129504 Jun 6 2016 i686-unknown-linux-gnu-gcc-4.1.2*
-rwxr-xr-x 1 root root 16233 Jun 6 2016 i686-unknown-linux-gnu-gccbug*
-rwxr-xr-x 1 root root 27360 Jun 6 2016 i686-unknown-linux-gnu-gcov*
-rwxr-xr-x 1 root root 2809256 Jun 6 2016 i686-unknown-linux-gnu-gdb*
-rwxr-xr-x 1 root root 2809256 Jun 6 2016 i686-unknown-linux-gnu-gdbtui*
-rwxr-xr-x 1 root root 849272 Jun 6 2016 i686-unknown-linux-gnu-ld*
-rwxr-xr-x 1 root root 583552 Jun 6 2016 i686-unknown-linux-gnu-nm*
-rwxr-xr-x 1 root root 737536 Jun 6 2016 i686-unknown-linux-gnu-objcopy*
-rwxr-xr-x 1 root root 822656 Jun 6 2016 i686-unknown-linux-gnu-objdump*
-rwxr-xr-x 1 root root 540928 Jun 6 2016 i686-unknown-linux-gnu-ranlib*
-rwxr-xr-x 1 root root 225280 Jun 6 2016 i686-unknown-linux-gnu-readelf*
-rwxr-xr-x 1 root root 516536 Jun 6 2016 i686-unknown-linux-gnu-size*
-rwxr-xr-x 1 root root 516568 Jun 6 2016 i686-unknown-linux-gnu-strings*
-rwxr-xr-x 1 root root 737536 Jun 6 2016 i686-unknown-linux-gnu-strip*
-rw-r--r-- 1 root root 1577 Jun 6 2016 ptxconfig
-rwxr-xr-x 1 root root 5889 Jun 6 2016 scons*
-rwxr-xr-x 1 root root 5889 Jun 6 2016 scons-1.2.0*
-rwxr-xr-x 1 root root 16572 Jun 6 2016 sconsign*
-rwxr-xr-x 1 root root 16572 Jun 6 2016 sconsign-1.2.0*
-rwxr-xr-x 1 root root 48685 Jun 6 2016 scons-time*
-rwxr-xr-x 1 root root 48685 Jun 6 2016 scons-time-1.2.0*
-rwxr-xr-x 1 root root 6871 Jun 6 2016 xmlrpc-c-config*
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