Lightroom 4.1 not importing all photos from canon 7d

Upgrades to Lightroom 4.1 last weekend. 
Imported first photographs directly from Canon 7d (2.03 firmware)  copy as dng files through normal import process, and lightroom 4.1 fails to recognise approx 20-30% of the photos. (question mark in corner file location missing)
This has happened three times, Thought it might be a card format problem, but then opened lightroom 3.6 which is still installed on my computer, conected the camera and all files imported directly from camera into lightroom just as they alwways have.
So whats the glitch?
Neil

Rikk,
Thanks for the reply,
yes I have tried with a card reader and have had some mixed results, but always when I go back to lightroom 3 all the photos are seen and imported.
I reinstalled LR4 yesterday, upgraded to v4.3.
I have set up a new catalogue with none of my historic photo's, I will archive those in LR 3.6.
Have re-installed the latest firmware for the canon 7d,
Took some test photo's connected camera via usb, had to manually select import, the 7d was listed, then imported pics, no problem this time, need to see if this is consistent. Did the same with the Fuji xe1 and all 12 pics loaded.
Will try tomorrow with significantly more pictures from both cameras.
I wonder if there is any issue associated with importing the old catalogue from 3.6 and upgrading in LR4?
Enjoy New year,
Neil

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