The PortableApps Platform gives the folders Documents and PortableApps special qualities that make them differ from any other folder you create yourself on a flash drive. These special qualities can cause problems for other portable programs, e.g. PocketSearch (see my post http://portableapps.com/node/29630), which is a handy program to index and search the content of your flash drive. The folders Documents and PortableApps are invisible for PocketSearch.
It is not only the icon that gives these 2 folders a different appearance. It goes beyond that. For a test I removed the folder icons by deleting the folder X:\PortableApps\PortableApps.com\App\Graphics\WindowsFolderIcons. After doing that the folders look the same as any other folder but they are still invisible to PocketSearch. The only way to make them visible to PocketSearch is to delete them and then create folders with the same names (and move your data and apps back there).
What is the reason for this strange behavior of the preset folders Documents and PortableApps (and also of Music, Pictures, Videos)? Is there a way to fix it without deleting and recreating them?