Some four years ago, when I bought my first X-Pro1, I had a similar issue. I shot all day long and must have had over 500 images. I imported all files into LR ( believe it was LR4 at the time), removed the card, slid it back into the camera body and formatted the SD. And I was ready for my next shoot.
But when I began my initial scan of the images, a number of them didn't show. They must not have been imported. I went out to shoot again, this time only a few dozen. Same thing happened, not all images were imported!
I wasn't overly pleased with the camera anyway and had planned to sell it, so I didn't really worry. Never before or afterwards have I noticed such a loss of images during import. The missing images were clearly shown in the LR import display (and were checked). I made sure of that during my test.
Since then, I've again purchased another X-Pro1 (and have learned to like it) along with other X-System cameras. I still use my Canons and my Panasonic GF1. I haven't noticed such failures again and had forgotten about the matter until I read you mentioning it.
I don't know if the phenomenon could have been blamed on the camera, the SD card (which I doubt) or LR. But such failures clearly show, you need to check all imports. How to do this, I can't say. Probably assuring that 265 images shown in the import dialog are actually imported. But if only 260 are imported, do I have to repeat and hope LR recognized and doesn't import doubles? I hope I never encounter that situation again.
My experience may not help you find a solution to your problem, but you are (or were) not alone in this matter.
