Comment 4 for bug 412116

I am not sure I understand correctly: it still happens with Inkscape 0.47pre1? Could you attach an example drawing that illustrates your issue?

There is also a preference setting for gradients - 'Preferences > Misc > Prevent sharing of gradient definitions'. Could you test if changing it helps to solve your issue?

If it is not the same issue as in bug #165936, please revert the duplicate status.