I have seen similar things happen when you and the files are sitting on opposite sides of a Daylight Saving shift. The EXIF data in the files is still proper, but the file info shown in the OS directory gets compensated for in the time shift. I wrote it off as a Windows oddity.
I can see where this could confuse things in the import dialog for determining duplicates.
This would match my case as well.
The Photos in question were taken some three months ago (and in a different timezone to where I am now) and we have transitioned to Daylight Saving time as well.
So, what's the fix, any suggestions?
I don't think there really is a fix.
That said, I never start shooting with a partially used cards. After the images are transferred to the computer, the cards get formatted and the counter reset back to 1. When I import the images into Lightroom, it is always whole directories at a time.