There is a problem with the code in file PHPCrawlerLinkFinder.class.php around line 143:
if ($meta_base_url != null)
$this->baseUrlParts = PHPCrawlerUrlPartsDescriptor::fromURL($meta_base_url);
I have a site which has the following base url tag: <base href="/content/">
This is not parsed correctly, so no links on this page are recognized.
As I am only spidering one site, I hardcoded the $meta_base_url. But this is not a good fix.