When I flip an object, I'd expect all gradients to flip the same way, but they don't! it's the same with "rotate 90 degrees" and rotation by handles; gradients stick to the same orientation. As it works now, flipping an object horizontally does not give me the exact mirror image, since most gradients now look funny. Is there a technical reason for this behavior? I find it kind of counter-intuitive.
Yes, I'm working on that right now :) This is the case only with "optimizing" objects, i.e. paths and rects. As a workaround, go to Inkscape Preferences (if you're using CVS), Transforms, and click on "Store transformation: preserved". This will fix this problem for all objects.
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