As you noted, the logarithmic scale skews it right, because the number of nonces within log(10, nonce) > 9 is 3 times larger than log(10, nonce) < 9
The other factor that might skew the nonces on your chart is that a pattern in the nonces on the blockchain doesn't necessarily mean that it's caused by a problem in the mining algorithm. As a trivial example, imagine if I wrote a mining example that never searched odd nonces. This wouldn't affect its mining power, but a person looking at the output might conclude that odd nonces never produced blocks.
As a more realistic example, mining clients spend more time searching low ranges of nonces than high ranges of nonces, simply because they start at 0, and reset every block. This effect becomes less pronounced over time as hashpower per mining client increases.