I have plogger installed on a subdomain of my main site. Therefore, things like the RSS Feed, The slideshow link, etc etc are calling the base URL which right now is read as my main domain.
Is there anyway it can be changed to take into account for the subdomain
You should define the base URL in the installation, if memory serves (sometimes it doesn't). If you define it there, I don't see why it wouldn't properly generate the links.
Line 16 of plog-load_config.php $config["baseurl"] = "http://".$_SERVER["SERVER_NAME"]. substr($_SERVER["PHP_SELF"],0,strrpos($_SERVER["PHP_SELF"],"/")) . "/";
Try manually putting in your subdomain $config["baseurl"] = "http://sub.domain.com". substr($_SERVER["PHP_SELF"],0,strrpos($_SERVER["PHP_SELF"],"/")) . "/";
Why not use "HTTP_HOST" instead of "SERVER_NAME" ? I just changed it and works for me, I'm pointing some subdomains and several domain names to the same server, making them look like different web pages.