Think your problem may be with tracking file for these images, have a look at this post by ceroberts75:
You are no doubt already aware that the pictures you take with the camera are in the /home/user/MyDocs/DCIM folder and the pictures (jpg) files you save from email, etc, are stored in the /home/user/MyDocs/Pictures folder.
open terminal then do the following commands (each line below is followed with "enter")
then reboot your device???
It is not useful on my phone.
and after I did the above commands, photos that was supposed in gallery is gone now....omg!