PhpED 5 on Windows Vista, but the same issue happened to me on XP and with the previous version of PhpED also.
The problem is that after a certain amount of time working on a Project, the 'Save As' dialog window becomes out of sync with the actual file system. New folders (created using the Workspace Explorer and right-click 'New Folder' don't appear in the Save As window at all.
See the attached screen shot:
Here you can see that in the right-hand frame there is a folder called 'app'. But look on the left-hand frame, there is no 'app' folder present. The same happens for the 'yui' folder.
If I double-click on the 'app' or 'yui' folders in the right-hand frame nothing happens, the contents just refresh themselves.
The only way to save my file is to type in the full path into the 'File name' field (as you can see in the screen shot).
The problem fixes itself if I close PhpED completely and restart it.
The files are all stored on a server which is mapped to Windows as a network drive (drive W: in my case).
Using 'refresh' in the main Workspace Explorer works and picks-up the file system correctly. Only the 'save/load' dialogs are wrong.
Cheers,
Rich