Inkscape not saving editing svg properly

I have found that saving the SVG in Inkscape as a "Optimized SVG" with unticking the "Simplifying colors" check box seems to rectify the issue, I can confirm the outputted SVG files work as they should with those settings.

Not reproduced on Crunchbang Waldorf (a Debian stable based distro.), with Inkscape, Batik (squiggle) and the Thunar file manager. They all show a red shape.

But the affected path shows two concurrent attributes to describe its fill color:

  <path
     d="M30,53.999C12.056,53.999,6,47.943,6,30C6,12.056,12.056,6,30,6c17.943,0,24,6.056,24,24 C54,47.943,47.943,53.999,30,53.999z"
     id="path13"
     fill="#1080DD"
     style="fill:#ff2a2a" />

Modifying the color in Inkscape changes the style, but not the fill attribute. Depending on the precedence used by your application, you can have a blue or red shape. I haven't checked the specifications yet, but I'd tend to consider Batik as very accurate. To be confirmed.
IMHO, Inkscape should get rid of the old fill attribute as soon as the color is changed anyway.

Another workaround: remove the fill="#1080DD" line in the SVG file with a text editor or the embedded XML editor.

<quote>
For user agents that support CSS, the presentation attributes must be translated to corresponding CSS style rules according to rules described in Precedence of non-CSS presentational hints ([CSS2], section 6.4.4), with the additional clarification that the presentation attributes are conceptually inserted into a new author style sheet which is the first in the author style sheet collection. The presentation attributes thus will participate in the CSS2 cascade as if they were replaced by corresponding CSS style rules placed at the start of the author style sheet with a specificity of zero. In general, this means that the presentation attributes have lower priority than other CSS style rules specified in author style sheets or ‘style’ attributes.

User agents that do not support CSS must ignore any CSS style rules defined in CSS style sheets and ‘style’ attributes. In this case, the CSS cascade does not apply. (Inheritance of properties, however, does apply. See Property inheritance.)
</quote>
<http://www.w3.org/TR/SVG11/styling.html#UsingPresentationAttributes>

Related issue (when modifying the color of gradient stops):
- Bug #1075325 “inkscape does not remove stop-color attribute from lineargradient tag when modified”
  <https://bugs.launchpad.net/inkscape/+bug/1075325>