In Mac OS X Mavericks, the Finder no longer passes the "-psn" flag to applications. In ImageJ.c line 1613, the launcher checks for the -psn flag to determine if it should chdir into ij_dir or not. Since the flag is no longer passed, it never happens. I think the chdir should happen regardless of whether the app was run from the Finder or not, so just moving the chdir on line 1624 outside of the if statement should work.
In Mac OS X Mavericks, the Finder no longer passes the "-psn" flag to applications. In ImageJ.c line 1613, the launcher checks for the -psn flag to determine if it should chdir into ij_dir or not. Since the flag is no longer passed, it never happens. I think the chdir should happen regardless of whether the app was run from the Finder or not, so just moving the chdir on line 1624 outside of the if statement should work.