XF 1.5 Crawled urls not including base ref, so giving 404 errors


I'm checking our server logs and limiting 404 errors where possible. I can see that we have several 404s that result from the url base ref not being included, so I'm wondering if I have a configuration issue or what we can do about this.
So our base ref includes a forum directory - www.ourdomain.com/forum/ and in our page source, I can see that this is listed and included in the <head> like
<base href="https://www.ourdomain.com/forum/" />
and references to styling and other files are in the page source like
<link rel="stylesheet" href="css.php?css=uix,uix_style&amp;style=5&amp;dir=LTR&amp;d=1523529034" />
<link href="favicon.ico" rel="icon" type="image/x-icon" />
now this seems to render in the browser ok, but I can see that because the base url is not implicitly included, it's being crawled in 2 ways:
either the location is just added to our main domain, like www.ourdomain.com/css.php or it's added to the entire url of the post, like www.ourdomain.com/forum/threads/post-title.268124/css.php , neither of which are valid.

We get the same behaviour with stuff within threads, so things like quoting, watching, permalinks within posts, are all in the format
<a href="threads/title-of-the-thread.268124/" title="Permalink" class="datePermalink">
So some crawlers add this just onto the domain rather than including the full base ref url which includes the /forum/ directory.

Can anyone suggest how we can force the base ref to be included in our page source?


no ideas?
in contrast, if I look at the page source of this page here, I see that there's a leading slash on urls of links and included items.
eg: <link rel="icon" type="image/png" href="/community/styles/default/xenforo/xenforo-favicon.png" sizes="32x32" />