Hi Pablo Laguna and majhul,
we have introduced a new WordPress hooks to look for Footnotes short codes in the Post object after collecting it from the WordPress database. This hook seems to be necessary for Custom Post types.
In your case, this new Hooks counts the Footnotes twice as seen in the Reference Container.
`1., 4., xxxxxxxx
2., 5., xxxxxxxx
3., 6., xxxxxxxxx’
Therefore, the hyperlink between the Footnote index and the Reference won’t work.
I will fix that ASAP with a new release version. I will add an Excerpt mode so each customer can decide which WordPress hook should be used to look for Footnotes. The default will be the same as before 1.5.3 version.