Please simplify your code as far as possible and find values for the scale, that you can show the problem with a simple call of setAxisScale. Then try the same with a version without using the multi-axes patch.

When the problem is still there upload your demo code as it is and I will have a look at it. If the problem is gone without the multi-axes patch upload a tarball with your patched Qwt version too.

Uwe