1st I am personally new to joomla and this SEF comp. I don't get any money or anything for this, just want you to know that I am just a regular person using it like you. That said:
Uninstall the 1.4.0 version and download and install the 1.4.1 version. Don't try to use the upgrade for either the website or the file on your computer. No matter what I have not been able to get the upgrade function to work at all.
I have two sites that I am working on and a third on it's way. The original site I made is still using 1.3.3, don't have the heart yet to try the upgrade again, as I did with 1.4.0 and had to uninstall. But I think I might over the weekend. That way I can be sure not to lose my links as they are.
Now, the other site, I started it just the other day, so not many links at all and I uploaded 1.4 and it worked (ok) for the most part, but I just uninstalled it and installed 1.4.1 and it seems to be working a lot better.
I tried and tried many times using 1.4.0 on my 1st site with no luck at all. But this site really seems to handle the 1.4.1 version well. Will see in a few days about the dup. links etc., as to whether that issue has been solved, but so far, yep.
Even if you get your money back, I would still recommend using this comp. The only difference in the Free and Paid, from what I understand is the link back link at the bottom, which is not really a big deal, unless you require not having it there. But I think that you will be able to get the 1.4.1 version up and running very quickly on your site.
Don't know how new or old it is, and how many pages you have, but give it a shot. Might actually be what you want it to be.
Check out both of my sites here:
http://www.kccert.org - using the 1.3.3 version (seems slower to me)
http://www.disasterservice.org - using the new 1.4.1 version (seems a lot faster)
When you do view them using either IE7 or FF, as IE6 has an issue with my home page on my first site and I have yet to figure it out.
Good luck and I'll watch this post for a bit tonight and if I am on and you need help, I can see if I can help you. Just remember that I don't know sh** about this, as I am still learning on a daily basis.
Chris