I'm having the same problem now working on a book with over 1200 footnotes in Indesign CS6. It can be helped by specifying a page number for starting a section (lay-out, numbering and section options), but that isn't very handy: the first proof of the book will be reviewed by the author, so page shifts will occur.
Anyone got a better idea?
Check out my script. It can link section markers to paragraph styles. So
if you want your footnote numbering to start with 1 at the beginning of
each chapter, and you've got a paragraph style set up for your chapter
headings (presumably), the script will take the hard work out of setting
up the sections properly.
Under the "scripts" tab, look for a script called "Section Stuff".
I still had one problem: after using your script, I wanted to start page numbering after the table of contents, using roman numerals for the preliminary pages. (In the preliminary pages I didn't use the paragraph style where the section markers were linked to.) I ran into Zareeba's problem: the section started on the left page. (And the page frames shifted horizontally: left pages looked like right pages and vice versa.)
To solve this I first removed all section markers, using your script (just to be sure). Then I went to single page view instead of spread view and only then made new sections (for roman and arabic page numbering). Then I reran your script, this time without checking the box for removing existing section markers. Worked perfectly.
This may be a (late) answer to Zareeba.