system tests: Fix python crash during tests

As a developer i would like the system tests to not occasionally crash

This seems to be a python crash that takes a while to reporduce. After much testing first fixed a thread leak, but this was not source of problem. Real problem was calling an exception handler function that was a python object that had got garbage collected. We were using an earlier incantation of an exception handler replacement function that we had created, using the upstream one fixed the issue.