The 2016 CSDS installer adds one directory to the system path on windows: <INSTALLDIR>/Conformer Generator 1.0/bin
It does this so that the conformer generator can be run easily from the command line, without the need to specify the full path.
However, that directory also contains some libraries that cause the APEX software to crash if this location is used to find those libraries in preference to its own.
To fix this (at least on Windows 7, other versions of Windows will be similar), go to Control Panel, search for environment variables and click on 'Edit the system environment variables'. In the Environment Variables dialog, in the System variables section locate the 'Path' variable and double click on it. Locate in that variable the path to the conformer generator bin directory, e.g.
C:\Program Files (x86)\CCDC\CSD_2016\Conformer Generator 1.0\bin
and delete it. Note that all paths are separated by ; so be sure to ensure that you leave the entries before and after separated by a single semi-colon.
Click the various OK buttons to close all the dialogs. APEX should now work, but the conformer generator will need the full path to be run at the command line.