For reference, this looks like a clear description of the problem:
Probably not worth reading the whole thing, but one suggested solution that may work for you (assuming your $PYTHONPATH being set was not the issue) is to add this line to the top of your /home/cryosparc/config.sh file:
export PYTHONNOUSERSITE=true
Note that eval $(cryosparc env) will not cause this to be set in a new shell, so you should directly set this in a shell if you are going to try to use the cryosparc python. If you do export the variable in a shell and then do
eval $(cryosparc env)
python -c "import numpy; print numpy.version"
Then you should get the correct 1.11.2 version.
Let me know if this works.