Created attachment 25652 [details]
svg with three rectangles

To reproduce:

1) Have an FO file in which an SVG (I have only tested with external-graphics)

2) Inside the SVG, have a gradient defined and two elements e.g. rectangles. Set the stroke opacity of the first element to a value near 0. NOTE: The order is important - the stroke opacity must be set on the element preceding the gradient filled element.

3) Make the second element have a gradient fill.

RESULT: The second element's gradient fill will have the same opacity as the stroke of the preceding element.

** Possible cause **
This is due to Batik's GraphicContext.setPaint() method replacing the "foreground" Color attribute if it receives a Color instance as a parameter (due to a "paint instanceof Color" check). The "foreground" of the GraphicsContext is later used to set the fill opacity in the line inside PDFGraphics2D.fill() method:

applyAlpha(c.getAlpha(), OPAQUE);

However in this case, batik's GraphicContext.setPaint() is receiving a LinearGradientPaint object which does not inherit from Color. Thus it does not set the "foreground" attribute, meaning that an alpha from a previous setPaint() will be used - in this case, the stroke opacity of the preceding SVG elemnt.

** Possible hack **
Since the applyAlpha line in PDFGraphics2D.fill() will not be correct when the paint returned by getPaint() is a gradient, I added an instanceof check so that it only runs when getPaint() returns an instance of Color. This is not a thouroughly thought-out fix and therefore should just be regarded as a workaround hack.

Attaching SVG file and FO, plus hack (most likely not suitable as fix) to get around issue.