New portfolio items appearing smaller on the grid

Are your source images all of the same size ?

If you hover the src attribute for your images with the Chrome Developper Tools, it will tell you the natural size.

For the smaller images, the natural size is: 292 x 190, 400×260.
For the bigger images, the natural size is: 306×260 (all seem to have the same).

My best guess is that if you crop/fiddle with the size of your images, you might be able to get them at the right size.