s/Whispernet/Skynet/ ?
Err, nope, unless you moved them to a directory *inside* the linkss/screensavers folder, it definitely shouldn't be doing any magic directory recovery, especially if you're not using the shuffle feature...
You might try a fsck on the Kindle USB drive, but I'm not sure if it's actually useful...
A factory reset would re-create the userstore partition, yes. Although if it really exhibits FS corruption, who's to say it won't also affect the system partition?