Yep, happens for me too. One of those cute minor "oh this is so Kobo!" bugs I haven't bothered to mention here.
Simple workaround:
1) Open search in book window.
2) If it shows the previous book in the grey box near the top where it says "Book: ...", close the search window.
3) Open the search window again. Hey presto - correct book will be searched.
I have no idea what triggers this bug. I just tried it, and it gave me the correct book at the first attempt. Then I closed that book and opened another - and promptly the bug was there...
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