I have installed 'More Taxonomies' and tested this and you are right. The custom taxomonies do not show up. I delved a little deeper and realised that the custom taxonomies created by 'More Taxonomies' does not allow for the 'public' argument when creating custom taxonomies (there is no option for it in the advanced settings). I am not sure why, but my plugin loads the dropdown where 'public' = true and '_builtin' = false. If you remove the 'public' => true then it shows the taxonomy.
I assume this might confuse some people in future, so I will remove the restriction of only showing public taxonomies from the next release. In the meantime, you can edit the file 'gfcptaddon_1-5.php' or replace it with this code http://pastie.org/1734034
I hope this helps