I have noticed this happening more and more. I move an image folder in to my Pictures hierarchy that LR is managing. I then "sync" to get LR to recognise the folder and put in to Index... which happens OK.
However, If I sync again immediately, there are a whole bunch of other images that LR seems to count as needing importing, a small fraction of which actually seem to get re-imported again.
I've tried rebuilding catalogue - doesn't seem to be any different.
Are there perhaps some output images somewhere that are causing problems?