Thanks for the quick and precise answer.
I do use Markdown Extra mode processor, but here are my findings after reading your response:
Concerning the footnotes, they look good, but the links don't work. You can test this by putting something like 50 paragraphs between the footnote and its definition. They don't jump when you click on the links.
I have then exported my document to an HTML File using markdown pad 2 and found out that the link actually works fine in Firefox and Chrome, but not in IE Version 9 (windows 7), and not in the built in browser of markdown pad 2. So this seems to be a IE Issue (as always..)..
Concerning the abbreviations, in my document, I had defined them with a space on both sides of the colon as in
*[TBC] : To Be Clarified
I am developing a website using PHP. The "standard" markdown implementation in PHP accepts that and I used it only this way. After reading your response, I removed the space on the left side of the colon and realized that markdown pad 2 is also converting abbreviations this way. This seems to be a little discrepancy between Michel Fortin's implementation and description of this feature.