I'm just glad that footnotes are actually breaking for you, that's progress! Oh, actually, you're in single column mode, so that might have been an earlier fix... Are you running a recent version? (the last footnote changes relevant for this were fixed in early March this year). If not, please update!
If the problem is still there with a recent version, carry on reading.
So, there are several things that might be happening, and the only way to actually tell for certain is to spend about half a day reading lots of cryptic log files with the source code open beside you...
But, I can make a guess or 2....
You'll see that it is including the line needing the footnote, and then stops. So... for some reason it decided, having read the footnote, that the page was now full if it split the footnote where it did. It can make that decision in 2 different places: while reading the input or while laying up the text. If it made the decision while reading the input then there's no more input available to the 'laying up text' bit, and so you'll get gaps.
If the problem was in the second half, then... urm... I probably got some maths wrong somewhere in the code. It might also be that having placed the footnote, for some reason it decided that the ideal place to break the page was immediately after for some other reason.
I hope you don't have anything trying to alter footnote behaviour in your ptxprint-mods.tex file. If you do, please comment them out. I also hope that you're feeling brave... have a look at the Full view "Advanced" Tab, find "Show TeXpert hacks",on the bottom right:
and then go to the new tab that opens. Then there are some controls for you to play with:
* "Enhanced paragraphed footnotes" May help, I'm not sure. It's a "do things the old way" compatability flag, and I seem to remember it makes some minor changes to non-paragraphed footnotes too.
* Reducing the "Last note interline penalty" will tell the code that it's allowed to break the footnote in more places. (10000 should mean only break at paragraphs). For your sort of text-footnote ratio, you need it to be more like 500.
* "Footnote factor single column" could also be adjusted. Setting it to 0 will mean that it won't try to count footnote sizes at all during the "reading input" stage. That might cause other problems, but hopefully we've ironed those out by now. I'd actually try setting it to something like 900 (pretend it's 90%), so it's close to right, even though the original value is 100 (10%) for historical reasons...
* Last note: widowpenalty and Last note: clubpenalty values affect how bad it considers breaking before the last line and after first line of paragraphs in the footnote respectively.
* The various "split note" numbers are hopefully self explanatory... I'm not sure if they only apply to paragraphed notes or not.
If none of this helps, then sending me an archive is the best next step. I can't make promises about when I'll be able to dedicate the time to digging though.