I have been having the same problem with a blank screen (multiple book pages shown in right margin) with the premium version of Mantano (2.2.5) on my Nexus 7 and came here to look for solutions. I have done the same as you have with mixed success. When I shut Mantano down and restart my books sometimes reappear, sometimes not. I am transferring books to the device within Calibre 8.69 on Linux Mint 13 64bit KDE. On my Nexus 7 I use Calibre Companion to make the wireless connection to my laptop running Calibre. Once synced with Calibre I can transfer books from Calibre to my Nexus 7 device.
I do not understand what is going on...