Comment 3 for bug 774467

in the Preferences, under File->Inkscape Preferences->Transforms, if there is a check mark beside the item "Scale Stroke Width", try unchecking it to see if it helps. Otherwise, steps to reproduce would be helpful. How are you changing the x and y values. Are you using the X,Y,W,H spinboxes that are visible when you hit the Select icon (F1) at the top of the left side menu?