I don't think that's the case. I'm at GMT+11 and do not see any problems. From memory, the only timestamps the driver sets in the database are for shelves. The only confusion that could cause is when you sync to the Kobo server.
The file timestamps of the books will also be different, but as far as I can tell, these are not used.
What you could do to test this is disable the driver for a few connections and use "Save to disk" to put the books on the device. Calibre won't display the books on the device, but, it will help to determine if the issue is calibre or something else.
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