How long are you usually in the other app before you see this? The reason I ask is that what I believe is happening is that you have switched to the other app for 5 minutes or longer and then switched back to the Kobo app.
When the app has been suspended for 5 minutes or longer, we will check for an updated cloud bookmark, and this will cause the refresh you see, as potentially you may be in a different position in the book; for example, you suspended the app (you don't need to switch to another app, just suspend the app) on your iPad and started to read on your iPhone. After 5 or more minutes you then switch back to your iPad.
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