The affected markers are missing the inkscape:isstock="true" attribute in their definition. Not surprising since it's a new attribute added in 0.91 (rev. 11671) to fix Bug #165865 "Fix marker color on duplicate".
Adding the attribute to the SVG code manually fixes the issue, but it's only a workaround.
Thanks for the test file!
The affected markers are missing the inkscape: isstock= "true" attribute in their definition. Not surprising since it's a new attribute added in 0.91 (rev. 11671) to fix Bug #165865 "Fix marker color on duplicate".
Adding the attribute to the SVG code manually fixes the issue, but it's only a workaround.