Ah, yes, that was going to be my next question, sorry I missed that if you mentioned it earlier (and you did

).
If you're pushing books both to the internal storage and the sd card, the default "find the calibre database automatically" behavior will basically return the first one it finds, and there's potentially no real way to say which one that'll be (but I'd say there's a higher chance it'll point to the internal one).
So, that leaves you with having to manually set this up. This is done via the defaults.lua system. I'll direct you to the wiki for more details on how to make this persistent across updates, but, for now, check the defaults.lua file, in particular the section about SEARCH_LIBRARY_PATH
If you actively use both storage locations with Calibre, you'll probably want to use something like
Code:
SEARCH_LIBRARY_PATH = "/mnt/onboard"
SEARCH_LIBRARY_PATH2 = "/mnt/sd"
(To be tweaked if you use a more unconventional setup with the library in a specific subdirectory).
That should make things behave after a KOReader restart, and a single search will look at both "libraries" at once.