Hello Gonçalo Peres,
Yes, 0.9.5.4 was a very quick fix for this pagination issue introduced in 0.9.5. In fact, I just removed a function, which was added to solve this issue: http://wordpress.org/support/topic/same-post-in-different-urls
Now I have reworked it and hopefully I did not introduced a new bug.
The problem with "/category/name/page/1" is a different one and should be solved in the current development version too (0.9.5.5)
http://downloads.wordpress.org/plugin/polylang.zip