After enabling GENERATE_QHP etc, Doxygen was creating an index.qhp. However, one of the fields was created badly causing garbage to make it into the qhp file like:

<QtHelpProject version="1.0">
  <namespace>com.volumesoffun.polyvox</namespace>
  <virtualFolder>api</virtualFolder>
  <filterSection>
    <filterAttribute>doxygen</filterAttribute>
    <toc>
      <section title="PolyVox 0.2.0" ref="`º^L^A">
        <section title="PolyVox Framework" ref="index.html" />

Notice the text inside the ref="`º^L^A" where it should be ref="index.html"

I tracked this down to line 128 of src/qhp.cpp where the ref for this section is created. It was using the following code:

const char * const attributes[] =
{ "title", fullProjectname,
  "ref",   QCString("index")+Doxygen::htmlFileExtension,
  NULL
};

For some reason, about 95% of the time this will cause the ref field to contain garbage.

By changing it to be:

QCString ref = QCString("index")+Doxygen::htmlFileExtension;
const char * const attributes[] =
{ "title", fullProjectname,
  "ref",   ref,
  NULL
};

it seems to have reliably fixed it.

I don't know why the original version didn't work but this new version fixes it for me.