Web-server and rtorrent user must have read+write permissions to rutorrent/share directory (and to all files/folders inside it).
This was my problem. I did the following when i originally setup rutorrent
chown -R rtorrent share/
chmod -R g+w share/
chgrp -R apache share/
giving apache and rtorrent write permissions, to share, since apache is the group owner
However, after further investigation, what happens is rutorrent (the php, so apache user) creates folders inside the share/ folder, for each user such as "tom" or whatever, then inside there it creates various folders for settings and data for the plugins etc. Since these folders were created by apache user, they are OWNED by the apache user, hence rtorrent will not have write access to these folders that rutorrent has now created AFTER your initial setup.
So the solution is, have a cron that runs the 3 above chown/chmod/chgrp commands so the 2 users will always have correct access regardless of who created the files/folders. Or blanket 777 for everything. I believe the later to be overkill as I use my server for a lot more than rtorrent and dont want to compromise it.
One more solution I just thought of that is a bit tricky, is to add the rtorrent user to the "apache" group in /etc/group, so if folders are writable by apache group, then rtorrent will also able to write there.
Thanks for helping me track it down Novik and I apologise for wasting your time. But if possible, could I get some info on the update.php scripts as mentioned earlier? I am curious to know what I might gain by adding it in like other users on this forum have done.