Footnote IDs have random strings added since https://drupal.org/node/194558 in order to avoid duplicate IDs on pages which contain more than one node with footnotes. The problem is that with the addition of a random string footnotes no longer have stable IDs which can be linked.
Most sites do not have mutliple nodes with footnotes per page. Solution: make the addition of random strings to IDs optional..
Needs review
3.1
Footnotes