I apologize for the slow reply. Many of us were on winter PTO for the holidays until today.
I can't immediately reproduce the problem you describe. I do know Apple has made lots of fixes that improve the import experience, when importing directly from an SD card like I think you are. Could you please try updating to the latest iOS release, and see if this improves? If not, does an app re-install help?
Especially after a fresh app install, the numbers should really be close. The last time I experienced something like this, it was from my iOS filesystem becoming corrupt somehow. I fixed it by doing a full iTunes Backup and then a subsequent Restore. I know it's time-consuming, but I urge you to give it a try.
Just curious -- what is your iOS version currently installed, and what device are you using?