Sounds like your SD cards might be, err, problematic. Fakes? I've done this with several brand new Sandisk 128GB cards and a couple Crucial SSD drives. All were precisely the same size. I suppose, if there is some difference, you should just use a larger size card for your backup. You can always expand the FAT32 partition and filesystem (with idiot-friendly gparted, if you like) afterward to fill any unused space.
I'd be curious to see the output of fdisk on these variable sized cards advertising the same capacity.
What brands are they?
Of course, I was saying you should back up the whole card if=/dev/sdd, which gets every single block on the disk, preserving emummc and partition layout, rather than do each partition as separate image file (if=/dev/sddn of=./partn.img , where n=1,2,3...) and write each image file one at a time to a newly partitioned card. sdd is just an example, your drive letter will vary.