The first bug was just the beginning :D

Look at the white wire. Do you see any power source?
ProjectRed version - 1.7.10-4.7.0pre8.92

Bug is related to very intricate timing differences, which determine the order in which signals travel through wires. Might not bother fixing it, because this is a very tough one to sort out, and once the circuit compiler is finished, this won't be an issue.

By the way, the circuit would work if the repeater (next to the 4x4 array) is placed next to the top row instead of the bottom.

Example:
T - Transparent latch
C - Null Cell
W - Yellow insulated wire
R - Repeater

Like this:
T C C C W R
C T C C W
C C T C W
C C C T W

Instead of:
T C C C W
C T C C W
C C T C W
C C C T W R

Heh. When I moved repeater to top, two ghost signals ('1' and '2' wires) appeared :)

Remove that line of bundled cable and place it down again, it should fix that ghost signal.

Might be caused by an actual bug, or just some glitch in the Matrix, but until you give me steps to reproduce, can't really fix it.

I can give you exact IC BP where it is reproductible. This ghost signal does not stay constantly. It appears and disappears at reproductible conditions. Unfortunately I do not know what exactly causes this signal to appear, but in my IC it can be reproduced very easily.

Ok, give me the IC diagram and what causes it, and let me try to reproduce it.

I what format? I can dump NBT, can take PNG screenshot, can set up test server.

The world file will be the most accurate/easy.

~~ removed ~~

To reproduce: open blueprint in editor, give some pulses to left input and look to 4x4 array of cells. When counter state changes from 1 to 2, white wire remains active thus giving '3' output.