App location: iPhone / iTouch eBooks, ROMs not showing up after install

After relocating your application directory (manually, or with
BossTool) some packages are installed into root. (as opposed to the
mobile directory)

Using an SSH program:  (for example, CyberDuck)

To correct this, these files must be moved from [example]

private/var/root/Media/EBooks

To

private/var/mobile/Media/EBooks

Same for

private/var/root/Media/ROMs

(Frotz, PDF, other folders, at this time, leave alone.)

Still an issue?  File/folder permissions maybe the cause...