I have my "Documents" folder linked to a directory on a different hard drive.
Freemind cannot see/access/or follow the link from its file open/save dialog boxes. If I filter the dialog box on "all files", the link(directory) shows up as a file, but it is not accessible. I even tried manually typing the path, but I get an error that the attempt to save failed.
On the other hand, that link works just fine with with Freeplane. It is visible and saving, opening, navigating, etc. all function normally.
Glancing over this, it would seem like a software(Freemind) problem, but I am almost positive I have seen something like this before as related to something else in the OS. I just cannot remember what it was related to and all the searches I have done have been useless because of the commonality of the key words.