I did have something like that with my N905 Touch. The card wasn't recognised properly at boot time. To see the books, I had to eject and insert it again.
I'll have to play with my devices and see how they are behaving. But, they all have books in the main storage. Removing them isn't really possible as some are purchased from Kobo and they are downloaded to the main storage unless it is full.
How long have you waited before tapping the screen? And how many books are on the card? The more books, the longer the scanning process to look for the changes. That might be affecting when it updates the home screen.
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