The bad news is it appears to be a genuine bug, and as such you're pretty much limited to trying to work around it inthe sort of way you have been. You are not alone in seeing this, but I've not seen any reports, that I recall, that have pinned down the exact trigger.
This issue has been pestering me since the introduction of footnotes: CS2.
Never found "a solution" either. It seems the page composer just shrugs at times and gives up. (The same as it sometimes does with tables.)
We also have this problem ...
We are concluded, (??) When there is a note on the first or second line that starts in the block, justification and rebuilt and the problem happens! even made to change color of text on the blank page occurs ... our solution to an extra line at the beginning of the block without note or make it past the note on the previous page ...
when in a true solution?
Translation from French
Nous avons aussi ce problème …
Nous somme arrivé à la conclusion, (???) quand il y a une note sur la première ou la deuxième ligne qui commence dans le bloc, justification et refaite et le problème arrive !!! même le faite de changé de couleur sur du texte les page blanche survient … notre solution mettre une ligne supplémentaire en début du bloc sans note ou faire passé le note sur la page précédente …
à quand une vrai solution?
There is nobody here who can tell you when a bug will be fixed for sure. Adobe does know about this one, and the best I can suggest is that you give the CS6 trial a run when it becomes available, rumored to be sooner rather than later, to see if they managed to solve it for the new release. If so, there's a (very small) chance the fix will be included in a final patch for CS5.5, but I wouldn't expect to see it for anything earlier.
Many thanks for all the feedback -- at least it is reassuring that Adobe does know about the bug. On the downside, if it hasn't been fixed during the last three or more releases, it'll take quite a bit of hoping !