Double extending pistons act differently at different Y values. (As far as I can tell)

Long story short(ish), I remade CNB's famous compact 3x3 piston door so that it is the same compactness and works in 1.5. I have a super flat world made of Cyan clay, where the ground is at Y=60, and when I first made the door, it worked fine (above ground, so I had extra space, the bottom piston is located at Y =61) . But when I tried to move it underground, i noticed the pistons were acting differently. I've narrowed it down to the part pictured in the images (i've made a simple clock to keep them running so you can see which piston is extending). So when the door was above ground, the TOP piston extends and retracts quickly, leaving the block on it above it, which is the basis behind closing the door.

What actually happened was below ground (Bottom piston at Y=57), the BOTTOM piston extends, which pushes the top piston up, and renders my door useless

Steps to Reproduce:
1. Simple clock, into a monostable circuit, then feed that into a diamond of blocks.
2. redstone in the center of the diamond, torch opposite the input from monostable circuit, and a redstone above the block above the torch
3. activate clock.
4. rinse and repeat at different Y coordinates.