I have created a table of contents page using \tableofcontents and I have enough chapters and sections that it fills an entire page and goes into another.

The problem is that since it takes a second page all of the page numbering is off by 1.

Is there a way that I can fix that?

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Welcome to TeX.SX. On the first run the table of contents is not written; on the second run it is, but its appearance may offset the page numbers. On the third run all will be correct. –  egreg Dec 19 '11 at 17:30
I tried ScribTeX and it seems that adding \usepackage{lastpage} forces the process to do the required runs of LaTeX when the ToC occupies more than one page. Maybe it's better to put the reference to ScribTeX in the question. –  egreg Dec 23 '11 at 10:15