[MiKTeX] PDF bookmarks incorrectly nested using pdflatex

[Izzy <Isa...@or...>]

When I pdflatex my document (from the command line) my pdf document bookmarks
are incorrectly nested. Sections are nested within other sections when they
should be at the same level. Within the contents page and main document the
nesting is correct. 

The screendump below shows the problem. The bookmark pane is on the left and
the contents page from the document on the right. Background and Aim and
Objectives have the same section level as Introduction, but in the bookmarks
pane they are nested within Introduction.

http://www.nabble.com/file/p23079452/pdflatexproblem.png 

I am using MiKTek ver 2.7 and pdfTeX version 3.14... 

I have set the following hyperref options:
\usepackage[colorlinks=true, linkcolor=black, citecolor=black,
urlcolor=blue, bookmarks=true, bookmarkstype=toc, bookmarksopen=true,
pdfstartview=FitH]{hyperref}

I have tried removing and changing all these options, removing the .aux .log
.out and .toc files and also adding \clearpage after each section but the
problem persists. 

Sometimes, when I have edited the document body, the error in bookmark
nesting changes (different sections are incorrectly nested) and occasionally
it goes away, but never permanently. 

Please, can anyone suggest a solution?
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