Random unwanted space between paragraphs

I ran your code. (By the way, your not-so-minimal example doesn't compile unless the natbib and pagenote packages are loaded as well.) At least in the example you provide, there's indeed a problem of "overstretched inter-paragraph glue", confirming @Marco's guess. I can think of three solutions to this problem:

• You could issue the following command in your document's preamble:

  \raggedbottom

  This will let the height of the textblock vary from page to page. If your document is going to be typeset two-sided (aka bookstyle) with facing pages, the result may look poor from a typographic perspective.

• A more elegant solution (from a typographic perspective) consists of inserting the command

  \usepackage[bottom]{footmisc}

  (also in the preamble). Doing so will insert additional whitespace between the main text and the footnote rule rather than over-stretching the inter-paragraph glue. Of course, if a given page doesn't have any footnotes and features a single paragraph break, this approach won't help.

• A third and, in my view at least, even better solution would be to break up the text into more but shorter paragraphs. Doing so would increase the text's intelligibility and lessen the risk of an occurrence of the problem you describe.

  The example code you provide has an entire page consisting of only two, extremely long paragraphs, plus a rather long footnote. If you were to break up each of these two long paragraphs into two -- better yet, three -- shorter paragraphs, LaTeX would have many more degrees of freedom to play with while building up the page, thereby much reducing the likelihood that LaTeX will have to resort to over-stretching the inter-paragraph glue.

I also have this problem. I do have footnotes and don't use \par.

tried \usepackage[bottom]{footmisc} - didn't do anything

then tried the inelegant \raggedbottom - worked

By the way, in my case the last page only was acting up ...