Same problem here.
1.1.4/BL4.6 OOTB, used iLiberty v1.3.0.113 for jailbreak, activation, downgrade BL to 3.9FB, and unlock BB 04.04.05_G.
I have tried various options (Cydia / Installer & BSD subsystem).
I really don't think that I messed anything up, since it's a brand new phone and I have tried it a couple of times from a fresh restored 1.1.4. I rather think it must be a bug in iLiberty+
I guess I fixed it... it must have something to do with moving the Applications folder (to save space) with a symlink, but in a sloppy way, making the Applications folder invisible.
The trick that helped me is to redo the symlink (cf.
http://www.iphonestalk.com/how-to-fi...y-iphone-apps/), and to (re)make the Applications folder using WinSCP itself.
Check: the original symlink does work 'half' in WinSCP when you click on it (and gives the error posted above), but it doesn't properly show up when you type
# cd /
# ls -la
So I copied the Applications folder:
# cd /
# cp -
pr Applications /var/root
and then made a new 'Applications' folder using WinSCP (right-click > New > Directory) in both / (root) and /private/var/root (this gives an error, but never mind: after doing so, the Applications folder does suddenly show up nicely in the WinSCP GUI), and (re)created the symlink:
# ln -s private/var/root/Applications /Applications
Now all is working as expected. Hope this helps someone else with similar problems too.