Isabelle typically gives a warning when you try to run it on a 64bit machine:
### Cannot execute Poly/ML in 32bit mode (missing shared libraries for C/C++) ### Using bulky 64bit version of Poly/ML instead
On my ubuntu installation, the fix was to do the following:
sudo apt-get install lib32stdc++6
Hopefully this will be useful for someone! I couldn't find the answer on the web.