Footnotes move around between saves?

I’m sure I can’t be the only person with this problem, but a quick search of the support forums doesn’t come up with anything–apologies if I’m inadvertently duplicating something.

I’ve been having problems with footnotes and comments moving around in my saved text in Scrivener. For example, I typed in the phrase “Stephanie Smith, a researcher…” with the underline corresponding to the text I highlighted and tagged with a footnote. When I re-opened the program and file the following day, the highlighting and associated footnote had shifted to “Stephanie Smith, a researcher…”. When I compile and export the text, the numeral stays there, randomly hovering in the middle of the word “researcher.”

Is there something I can do to fix this without switching to inline footnotes, which I dislike, visually? It’s a giant pain to have to go back and manually fix this every time.

I’m using Scrivener 2.3.1 with Mac OSX 10.7.5 and paired with Endnote X5. I use in-text citations, so my footnotes and comments contain regular prose text only.

I’m fairly sure this has been mentioned before, though I can’t presently find where, and I can’t remember what was done about it. Anyway, it is quite a good idea to look at the latest beta:


That will have the latest fixes. it is safe to use – in fact I normally use the latest beta all the time.

Cheers, Martin.

PS – yes, the latest beta has this noted: “Added code that should avoid most situations (which are rare anyway) where linked comments and footnotes can get shifted because of RTF errors.”