Okay, I learn something new every day, which is excellent. Joomfish, and presumably most other multi-language support extensions, changes the base URL to reflect different languages. So in your example your base URL for English will be:www.mysite/en/index.php
and your base URL for Greek will be:www.mysite/el/index.php
I have to think about this some more to determine what the best solution is.
In the meanwhile, I recommend not using the Add Canonical plugin. Instead, you could use the og:url tag to point to a single language. This will cause your English Likes to show up on the Greek URLs and vice-versa.
I have attached a modified version of the plugin that will add the og:url tag which will point all of your Greek pages to the English version. If you prefer it the other way around just reverse the languages on lines 155 and 156.
This version can also be used by anyone else looking for multi-language support with minimal changes.
Anyway, let me know if you have any problems with this.
[edit: attachment removed. functionality is now included in the plugin]