Comment 1 for bug 626608

Can you attach your extension files? What platform are you working on, with which Inkscape version?

When testing this type of 'id' (an URL with sub-directory, using a slash) with an existing 'effect' extension (a copy of 'Modify Path > Scatter...' in ~/.config/extensions):

<?xml version="1.0" encoding="UTF-8"?>
<inkscape-extension xmlns="http://www.inkscape.org/namespace/inkscape/extension">
  <_name>Scatter (LeWitt) python.mysite.com/svg2css</_name>
  <id>python.mysite.com/svg2css</id>

Inkscape stores the settings in preferences.xml inside a group like this:

    <group
       svg2css.follow="1"
       svg2css.grouppick="1"
       svg2css.pickmode="rand"
       svg2css.toffset="0"
       svg2css.noffset="0"
       svg2css.space="5"
       id="python.mysite.com"
       svg2css.duplicate="1"
       svg2css.copymode="copy" />
  </group>

Inkscape does launch after a restart without error reading the preferences file and also correctly loads the previously used settings for the extension dialog.
(tested with Inkscape 0.48+devel r9731 on OS X 10.5.8)