Books has been updated (to 1.4-r469) and is rather unstable.
To continue using Books (the new version) with SwirlyMMS, you have to remove the old symbolic link, then create another one as it seems that Books has finally been updated to work according to 1.1.3+ firmwares (root vs mobile).
In WinSCP, go to the current EBooks directory:
Then at the top, click on "Commands" -> "Open Terminal" and type in: rm MMSFiles
Once completed, right-click on "EBooks" and click on "Move To..."
In the move field, copy and paste:
Then go into the newly-moved "EBooks" directory/folder (located in /private/var/mobile/Media/ and click on "Commands" -> "Open Terminal" and copy and paste:
ln -s /private/var/mobile/Media/MMSFiles /private/var/mobile/Media/EBooks
Click "Execute" and that should be it. Restart your iPhone (just to be safe).
And once again, if you ever wanted to remove the symbolic link, make sure that when in WInSCP, you are in the "EBooks" directory:
Then go to "Commands" -> "Open Terminal" and type in: rm MMSFiles
After that, you can delete the "EBooks" folder provided that you do not have any ebooks installed.