Comment 3 for bug 169019

Testing with Inkscape 0.47, 0.48.3.1 and Inkscape 0.48+devel r11572 on OS X 10.7.4:

a) Pattern:
Reproduced when switching from a flat stroke color with reduced alpha to a pattern.
Not reproduced when switching from a flat fill color with reduced alpha to a pattern (existing 'fill-opacity' is dumped, the value is reset to '1').

b) Gradients:
Reproduced when assigning a gradient via gradient tool on--canvas (affects both fill and stroke equally).
Reproduced when switching a flat stroke color with reduced alpha to a gradient via 'Fill & Stroke' dialog.
Not reproduced when switching a flat fill color with reduced alpha to a gradient via 'Fill & Stroke' dialog (existing 'fill-opacity' is dumped, the value is reset to '1').

Note:
AFAIU the 'fill-opacity' and/or 'stroke-opacity' properties may be present in the style attribute or not (represented in Inkscape by the 'Alpha' sliders in the color chooser for flat fill/stroke colors), and can not be edited from within the GUI as long as the object uses a paint server like gradient or pattern for fill and/or stroke. The issue could also occur when editing SVG files created outside of Inkscape.

Gradients:
The opacity slider of the 'fill&stroke' dialog adjusts the 'stop-opacity' value of selected gradient stops. The 'Alpha' slider (for fill-opacity and stroke-opacity) is either
- disconnected from the corresponding value in the 'style' attribute (current stable)
- or linked to the global opacity slider (latest trunk r11572)

An alternative solution for bug #1028425 (changes committed in r11572) might have been to keep and fix the separation of 'fill-/stroke-opacity' (via 'Alpha' slider) and 'stop-opacity' (via 'Opacity' slider) in the Fill&Stroke dialog, instead of linking 'Alpha' to the global 'Opacity' slider for the special case of editing the style properties of selected gradient stops. OTOH, there is no correspondent solution for pattern fills.