I have an idea. Make sure that in your report template you at least have the following three div's:

<div class="header"></div>
<div class="page"><!-- content in here --></div>
<div class="footer"></div>

If your report template doesn't have these div's, it will display in HTML, but not in PDF, because wkhtmltopdf needs to know where to find the header and footer of a report.

I hope that this fixes your problem. Please comment if this isn't the solution.