First of all the Physics.
The velocities in the constant acceleration kinematic equations are instantaneous velocities at the initial time equal to zero, $v_{\rm i}$, and and final time $t$ when the velocity if $v_{\rm f}$.
In the first equation that you used you made no use of the velocities other than stating that the initial velocity is zero and so that is the correct value of $g$ from your experimental data.
In the other two equations you assumed that the final velocity was $\frac d t$ which is in fact the average velocity assuming the ball started from rest.
For constant acceleration starting from rest the final velocity is twice the average velocity.
As the average velocity is $\frac {1.0}{0.4003} = 2.498\,\rm m/s$ then the final velocity is $2 \times 2.498 = 4.996 \,\rm m/s$.
This gives the acceleration of free fall $g = \frac {4.996}{0.4003}= 12.48\, \rm m/s^2$ as you found using your first equation.
Now on to the experiment which is difficult to comment on as the actual experimental set up has not be described in any detail.
Perhaps the first thing which need to be done is to get an estimate of what the "expected" time for a free fall of one metre using ?
This works out to be $\sqrt{\frac {2}{9.8}} \approx 0.45 \,\rm s$.
As the timing device itself seems to be of a high precision and probably of a reasonable accuracy the discrepancy of $10\%$ in the timing points to a flawed experimental arrangement/technique.
There are numerous ways of doing this experiment in the school/college laboratory but if you are able to drop the ball from rest from a fixed position I suggest that using your apparatus you try the following.
Have the first light gate a distance $D$ from the position where the ball is dropped and the second light gate at a position which is $D+d$ from the initial position of the ball.
Again measure the time interval between the ball passing through the first light gate and then through the second gate.
That time interval $t$ is the time it takes for the ball to travel, from an unknown but constant velocity $v_{\rm i}$ when at the first light gate, a distance $d$, to the second light gate.
$d = v_{\rm i} t + \frac 12 g t^2 \Rightarrow \frac d t = \frac 12 g \, t + v_{\rm i}$
Keeping the first light gate at the same position (ie keep $D$ constant) move the second light gate to a new position and hence a new value of $d$ and again measure the time interval.
You now have two equations and two unknowns $v_{\rm i}$ and $g$ and hence you can now solve for $g$.
Perhaps a better method of analysis might be to plot $\frac d t$, which is the average velocity between the two light gates, against $t$ and from the gradient of the graph ($=\frac g 2$) find $g$?
If you want any further help then perhaps you need to say more about the experimental set up that you used?
It may be of interest to you to you that your method is the basis of the method used by D R Tate to measure $g$ at the National Institute of Standards and Technology (NIST), then called the National Bureau of Standards.
The paper is worth reading just to show what needed to be done to get a value to $\pm 0.00005\%$.