Ok, basically, here's what's happening. neskaya.net and subdomain.neskaya.net use separate virtual hosts in the configuration of the webserver. Each virtual host has its own "DocumentRoot" directive, which means that / refers to a different folder on the server, depending on whether it's called from the subdomain or otherwise. Example:

Code:
NameVirtualHost *
<VirtualHost *>
    ServerName "neskaya.net"
    DocumentRoot "C:/htdocs/neskaya"
</VirtualHost>

<VirtualHost *>
    ServerName "subdomain.neskaya.net"
    DocumentRoot "C:/neskaya/subdomain"
</VirtualHost>
Let say you have a link with the href attribute: "/referrers/click.php". In the main site, the webserver will serve the file from C:/htdocs/neskaya, while in the subdomain it will try to serve from C:/neskaya/subdomain. I can think of a couple of solutions for the problem, though neither is particularly elegant.

The first and most obvious of the two is to include a full path in the href attribute of the links in the subdomain, i.e. have href="http://neskaya.net/referrers/click.php" in the problematic anchor tags. This way, you're disregarding the domain it comes from, but the potential drawback is that it makes it easier to be called from any domain. Why someone would want to do that is totally beyond me though and by looking at the current source, one can fairly easily figure out where the actual click.php file is hosted if they use their heads a little, so it's pretty much irrelevant.

The second solution is to write yourself a little redirect script and host it on the subdomain. You'd need to handle the referrer based on GET or POST variables and fairly heavily modify that referrer script, so it's probably not even worth it.