I have installed Remote System Explorer.
After creating a Remote Project via SSH, the project cannot be opened. This behavior is specific to Aptana Studio, since I can replicate it both on the Standalone and the Plugin. With vanilla Eclipse and Pydev, this doesn't happen and the project folders can be opened and browsed.
The error that seems to trigger the behavior is a bug relative to Remote System Explorer: http://old.nabble.com/Pydev-%2B-Remote-Systems-Explorer-p25408547.html This bug hasn't been yet solved. However, as written previously, vanilla Eclipse throws the exception but still lets you continue working on your project, while Aptana Studio simply closes the project.