I set an environment variable EM_SAVE_DIR=1 as recommended on the github page.... Though it was recommended for debugging purposes, the fact of the matter is that it caused the files to remain both in memory and in the correct location, such that the error now only gets thrown on executables that I mistakenly didn't have anywhere on my PATH (cmake, sh, and make).
Though at some point later today, if I get all these tests worked out for runner.py, I may need to ask about making it work on visual studio, which throws error 6 on not finding a correct file in the tmp directory, and seems to be ignoring EM_SAVE_DIR=1....