The release package was downloaded from the opencv website (as stated above, but I cannot have links in this reply) . I got the extra modules from github/opencv/opencv_contrib by downloading the files as a .zip, which might have been the cause of the issues.
I am using the recommended layout as above and have not mixed the source trees.
I have built RUN_TESTS (also in Release,x64) which failed to build, passing 35/120 tests (visual studio output with pastebin code: mVFSGPf9). Notably, calib3d exited with code 0xc0000374 rather than passing or failing, which probably caused the build to fail. I am also not sure how many modules may have required the tracking module to pass the tests, which I assume heavily influenced these results.