PyCharm cannot deal with Linux softlinks?

My project files are in /home/user/Project/my_project/. Project is a softlink to /media/disk_with_important_things, which is mouted manually after startup of the computer.

If I open /home/user/Project/my_project/my_file.py in the editor, set a breakpoint, and run the project, the file /media/disk_with_important_things/my_project/my_file.py is opened and the debugger halts at the correct line, but the breakpoint (red dot) is not shown. Now the file is shown twice: One tab shows /media/disk_with_important_things/my_proct/my_file.py and one the file /home/user/Project/my_project/my_file.py. This is really annoying. Anyone else experiencing this strange behaviour?

Cheers
Paul

P.S.: Arch Linux, PyCharm 4.5.1.