Comment 2 for bug 1288272

Reproduced with 0.47, 0.48.0, 0.48.1, 0.48.2, 0.48.3.1, 0.48.4 - could be as designed though (not sure): when dragging a gradient handle, the handles of other gradients are 'objects', and the option to always snap to objects has been intentionally enabled.

<quote>
Any gradient handle, if dragged close to a handle of another gradient, will merge with that handle (drag with Shift to prevent merging). Dragging such a merged handle will adjust any number of gradients attached to it. To separate merged handles, drag them away one by one with Shift.
</quote>
<http://wiki.inkscape.org/wiki/index.php/Release_notes/0.42#Gradients>

Merging of the gradient handles can be prevented by dragging with 'Shift'.