I had a fair bit of trouble getting PNDs working first of all as my SD card is ext2 formatted, and PND scanning silently failed until I'd chowned and chmodded everything - but that's only because I prepared the card before I got my Pandora. If you make it on the Pandora after logging in to it, ownership and permissions should be set correctly anyway.
As for getting it to recognise newly installed apps, I usually unmount then remount the SD card, which you can do from the right-click context menu for the SD card on the desktop background. If you were willing to risk it, you could probably get away with ejecting and reinserting the SD card, but I always prefer to unmount my cards beforehands.