I get this problem too. All my books were shown as 'on device' with 0.9.0 but on 0.9.1 and now with 0.9.2 about half of them are not shown as 'on device' when I haven't loaded or removed any books to the device.
As Greygor suggests I think it is something to do with using a metadata plugboard but I can't work out a pattern or reason. Like him I use a plugboard to put series information in the title. Some books in a series appear on the device OK other do not. For some a entire series is shown as 'on device', for others the whole series is not shown as "on device". They were all loaded to the device at the same time and all previous appeared in the library as "on device".