When your ovi maps ignores the preloaded maps, it is because of a bug that makes it unable of finding them on your media.
Try in xterm to change directory to the one where there are the .qf file and cities folder (should be /home/user/MyDocs) and start nokia-maps from the terminal: it should again be able to use its maps offline.
I haven't been able to find the origin of this bug, but possibly it is some third-party package. Somewhere in the forums I described how to make a .desktop file to get an icon that launches nokia-maps from the right directory. However, when I reflashed my device to Pr1.2 the bug was over. Not that I use nokia-maps too much: I prefer Sygic.