I installed PortableApps Platform 10.0 in C:\Temp\PAS. When I go to Windows Explorer I can see the PortableApps and Documents directories. But when I go to the C:\Temp\PAS directory from the command line all I see is the autorun.inf and start.exe. Why is this? 
Running on Windows 7 64-bit.
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Document directories are flagged as system folders to enable the custom icons. This would be your issue.
Use dir /a instead of just dir.
That did it!
On a command-line you can use
attrib -S C:\Temp\PAS\Documents(and the same for PortableApps) to remove the System flag, this should make them visible to the DIR command without the /A parameter, however this will remove the custom icon from the folder, so if you'd like to keep the icon you can add the +R parameter along with -S.Note: Despite the fact that attrib +R will set the ReadOnly flag on the folder the contents will not be affected (will still be writable), unless you also add the /S parameter (which enables recursive processing of the command).
Note-2: In the future the Platform Installer may set the custom icons this way by default.
~3D1T0R