I got it working. Seems that they are actually different. The modules/toolkits/packages in the repositories seem to be for octave 3.0 only. When I was running octave from the terminal it would choose to run 3.0 instead of 3.2 because it had both installed. This can be solved by running
instead of just
This however does not solve the fact that I couldn't use the packages. They are, however, fairly easy to install manually. Just download the packages you want from http://octave.sourceforge.net/packages.php and then from the octave prompt run
some packages may have other packages as dependencies but they should be listed in the package details page.
pkg install package_file_name.tar.gz