First off, make sure if you are using a base tag, that you use the [(site_url)] tag to specify the href property and that it appears before any src or href attributes in the document...
<base href="[(site_url)]" />
Next, make sure you don’t have any src or href paths hardcoded with http:// in it within your document content. This way, all links to content in your site will be accessed using the scheme specified in the man request from your browser.
If those two points are not the issue, let me know and I’ll help you figure out what else might be causing problems.