As 3deeguy mentioned this has to do with EL bone layer. I went ahead tweaked your file to address this and other issues with this rig (I'll send you a link to the file).
Problem: Eyes and mouth don't move with smart bone
1) Change Head bone layer settings: enable Allow nested layer control
2) Mouth and Brows layer -> Release Layer
Problem: Eye doesn't deform correctly with smart bone
3) Move pupils and eyes layers out of the EL bone and into the EL folder. Delete EL bone layer; smart bones will be deleted as well and need to be recreated (see below).
4) Set EL folder masking to Hide All.
5) Reposition the points in the pupil and eyes layer, both at frame 0 and in the HT action.
Problem: Eyes/Brows don't mask correctly on head turn
6) Change mask settings:
a) Head layer -> Hide All
b) Brows, EL -> Mask this layer
c) Face -> Add to mask
d) all others -> Don't mask this layer
Problem: Recreate smart bones in the Head bone layer
7) Created the following bones with angle constraints, zero bone strength: EL, Pupil, Pup Up
8 ) Create SB actions: EL, EL 2, Pupil, Pupil 2, Pup Up, Pup Up 2
9) In each action, set bone angle and reposition points in the Pupils and Eyes layers as needed.
The reason for the last fix is that nested layer control appears to work only with switches, groups, or empty bone layers. Also, from a workflow standpoint, it's better to put all the smart bones in a single layer. This avoids having to skip around in the layer palette when animating.