Original report:
v1.1 does mostly help by placing the footnotes at the bottom. However, it doesn't completely solve the problem. See attached jude.pdf where the problem persists on one page. Also, in a larger rendering I have noticed that there seems to be a lack of vertical separation between the text and foot notes (too big to attach here).
Response:
This sounds like confirmation of my suspicions that the problem lies in a poor interaction between marginfix and whatever package (be it built-in LaTeX or an external package) is handling your footnotes. I am completely swamped at the moment but will come back to this in a few weeks when things slow down at work. In a previous life, marginfix actually handled floats as well as margins. It may be that reviving some of that code is the way to go here.
Original report:
v1.1 does mostly help by placing the footnotes at the bottom. However, it doesn't completely solve the problem. See attached jude.pdf where the problem persists on one page. Also, in a larger rendering I have noticed that there seems to be a lack of vertical separation between the text and foot notes (too big to attach here).
Response:
This sounds like confirmation of my suspicions that the problem lies in a poor interaction between marginfix and whatever package (be it built-in LaTeX or an external package) is handling your footnotes. I am completely swamped at the moment but will come back to this in a few weeks when things slow down at work. In a previous life, marginfix actually handled floats as well as margins. It may be that reviving some of that code is the way to go here.