The JPATH_ROOT directory is correct but if an extension is using the PHP dirname( __FILE__) to recompute an simulate the JPATH_ROOT then they may have problems when a file is located in a Symbolic Link directory. In this case, the system return the physical path and not the symbolic link path.

If Zoo use all the time the JPATH_ROOT, this should not be a problem and it is garantee that you are located in the Joomla root direction either from a symbolic link path or a physical path depending the apache document root directory.

Here Zoo, didn't give any detailed information on the source and line of code that would have a problem in Zoo.
If you can get more info on the peace of code in Zoo that cause the problem, please post the info.