A couple of things: You might be better off with a floating axis, if your axes are moving around too much. A floating axis doesn't cross at a fixed value, but is positioned relative to the whole view. See CPTestApp for an example.
If you are sticking with your current system, it seems you might be setting the padding on the wrong layer. You can try the graph layer, but also the plotAreaFrame layer. It definitely should be possible to make it work.
Drew
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