The pattern you are noticing is that $9^{\text{th}}$ differences modulo $6$ are congruent to $0$ about twice as often as $2$ or $4$. So you get a bell curve of the values divisible by $6$ above the bell curve of the values not divisible by $6$.
A typical $9^{\text{th}}$ difference looks like
$$
p_{i+9} - 9 p_{i+8} + 36 p_{i+7} - 84 p_{i+6} + 126 p_{i+5} - 126 p_{i+4} + 84 p_{i+3} - 36 p_{i+2} + 9 p_{i+1} - p_i.
$$
Taken modulo $6$, we first end up with $p_{i+9} - 3p_{i+8} + 3p_{i+1} - p_i$. But in fact $3p_{i+8}$ and $3p_{i+1}$ are both congruent to $3$ modulo $6$, because all primes except $2$ are odd, so the $9^{\text{th}}$ difference is just congruent to $p_{i+9} - p_i$ modulo $6$.
Primes larger than $3$ come in two kinds: $p_i \bmod 6$ can be either $1$ or $5$. These are known to be equally common in the long run: we can think of it as a coin flip. They are not quite independent coin flips, but as $i$ gets large, $p_i$ and $p_{i+9}$ become pretty far apart and so we don't expect much correlation between $p_i \bmod 6$ and $p_{i+9} \bmod 6$. (But I'm not sure if this is proven or just expected heuristically.)
In the heuristical model where $p_i \bmod 6$ and $p_{i+9} \bmod 6$ are each independently randomly chosen from $\{1,5\}$, their difference $p_{i+9} - p_i$ is:
- $0 \bmod 6$ half the time: when we take $1-1$ or $5-5$.
- $2 \bmod 6$ a quarter of the time: when we take $1-5$.
- $4 \bmod 6$ a quarter of the time: when we take $5-1$.
The frequencies of $2 \bmod 6$ and $4 \bmod 6$ are about the same, so they form the lower bell curve together. (It looks thicker, because there are about twice as many points there.) Since $0\bmod 6$ has a frequency about twice as high, it forms a separate bell curve scaled up from the first.
In general, for any $k^{\text{th}}$ difference, we expect some effect, because if $(p_i, \dots, p_{i+k}) \bmod 6$ were evenly distributed on $\{1,5\}^{k+1}$, we can't evenly divide the $2^{k+1}$ possibilities between the three results $0$, $2$, or $4$. The difference is strongest when many of the coefficients in the $k^{\text{th}}$ difference are divisible by $3$; $k=1$ or $k=3$ actually have as strong an effect as $k=9$, and $k=2$ should be about as good as $k=6$.
The difference is also easier to see for larger $k$, simply because the interesting parts of the bell curves have more points! This explains why you might not have seen anything for $k=1$ or $k=3$. If we go up to $n = 50\,000\,000$, I can make out the two bell curves for $3^{\text{rd}}$ differences, but they don't look as nice as for $9^{\text{th}}$ differences.