Wrong URL used when accessing article through a module - joomla

I have an annoying problem and am hoping someone will be able to help.
We use quite a few extensions on our Joomla site (Roksprocket mainly but also Global News Filter for instance).
The modules themselves are working fine however when I click on an article in one of these modules the article opens but it doesn't use the nice URL that should be displayed (we have Search Engine Friendly URLs set to Yes and Use URL rewriting set to Yes). This happens for all modules that draw off a category (so I don't think its linked to a specific extension).
For instance on our Case Studies page if you click on Read More on the RSA Case Study you get this URL
http://www.assima.net/en/resources/case-studies/99-home/resources/case-studies/ats-case-studies/649-case-study-rsa
but what you should get is the menu item URL associated with this article which is this
http://www.assima.net/en/resources/case-studies/ats-case-studies/rsa
I don't think there is anything wrong with our .htaccess as I reverted back to the default Joomla one and it still occured.
Also this used to work perfectly. I first noticed it around October or November last year.
If anyone has any ideas I would really appreciate it, I've googled the problem many times and not found any help.
Thanks
Emma

FIXED.
Due to a Joomla bug. Fixed by overwriting the route.php file as described in this post: http://forum.joomla.org/viewtopic.php?f=625&t=831007&start=30

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