I'm not sure what else could be happening. I always have multiple books open and the reading %'s are picked up properly by calibre every time I connect. I'm assuming you have the correct boxes checked in the KU tabs.
I would use the Restore function in KU to set your two test books back 0%. Then just read a couple of books normally for a couple of days and see what happens.
If that does not work. I'm sure some of the local wizards here will chime in with advice.
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