Didn't do a thorough search, but looked through the main (tracker) post, and didn't see anything relevant. This behavior is weird (and VERY annoying).
Brand new install of PortableApps (16.0) on an empty flash drive.
No problem installing the apps, but as soon as I selected settings, several shortcuts appeared on my desktop (these were in no way related to PortableApps, they were applications and documents on my system). Removed the shortcuts, rebooted, and started PortableApps again. I could add more apps, and use them for hours with no changes (meaning no shortcuts appearing), but immediately after I clicked on settings in the portable apps menu, the shortcuts appeared again.