The log file shows this around the place where it occurs:
Underfull \hbox (badness 3482) in paragraph at lines 1685--1685 \T1/mdugm/m/n/10 lated from pre-cip-itable   Overfull \hbox (9.82391pt too wide) in paragraph at lines 1783--1788   ) (../5aims&objectives/aims&objectives.tex )  (../4data&methods/data&methods.tex  Chapter 2. <../figures/StudyArea.png, id=2314, 647.2983pt x 504.2037pt> File: ../figures/StudyArea.png Graphic file (type png) <use ../figures/StudyArea.png> Package pdftex.def Info: ../figures/StudyArea.png used on input line 57. on in put line 57. Package pdftex.def Info: Requested size: 455.24411pt x 354.60968pt on input lin e 57.
Specifically before you see chapter2 ^ . Here is my preamble, I don't think the problem is in it though.
It's between the end of a section and a new chapter, if that helps.