Actually, no. I removed firefox and reinstalled mozilla, but i figured out the problem after i done this and i think i can see how to relate it to firefox. I edited the file /usr/bin/mozilla to reflect the new location of my install. For some reason it had kept the old locations of the install that came with my distro.
For firefox i assume all that has to be done is the same.
Now i can open docbook files with mozilla and use the clickable links in my email without any problems at all.
Dont really know if how i done it was the proper way, but hey, it works!