I know correctly understand your problem, but I don't know
> how to fix it. It seems you need a pad setting for the
> distance from the axis label to the tick mark labels, but I
> don't see one in the rc file.
There is an Axis property LABELPAD that can be set -- it has not been
exposed to rc yet but should be. Something like
ax.yaxis.LABELPAD = 5
should work for now. Let us know ....