Libreoffice also messes up the format, and because it's a biology PhD the norm is not to use LaTex (which I think is only really used for Maths and Physics these days)

This mess is why I'm writing mine in libreoffice (started it in open office then upgraded ubuntu (and I just checked and it does mine fine)

Is Libreoffice managing to import it correctly or is that the problem?

As far as I can tell the problem here is the fonts, whatever solution you use is going to have to allow you to export the fonts along with the PDF. I had similar problems some months ago with PDF and Chinese characters where it just was not working correctly.

PDF itself wasn't designed with scientific writings in mind AFAIK and as a result you're not likely to have the necessary symbols included in the default software. You really should be fine if you include them with the export. No idea how to tell MS Office to do it though.

Libreoffice isn't importing correctly, it's messing up all the formatting and image positions. She's going to try booting it up in office 2010 and see if that can fix the problem.
I think the problem is coming from that it's been written over the last 4 years and on different systems so some of the equations seem to be set up using office 03.

*fingers crossed*

You might also consider taking screen shots of anything that does not convert. Crop the equations and insert in a standard image format at the same position the original equations were entered.

Edit: If the equations are many and located throughout the text you might screen shot the entire paragraph, delete the original, and insert the cropped image at the correct location. Conversions usually fail when code is encountered that the conversion program does not understand. The attached would convert easily as an image but may fail to convert where the equations code is encountered by the conversion program. An image would eliminate the equation coding.

But . . . with 300 pages to convert the task may not be worth it unless all else fails . . . =)

That's always going to cause problems. She might also try exporting the files as an ODF file rather than DOCX in case that doesn't work. There's also a few programs out there that can convert .DOC files into LaTex files, if she can get it into LaTex without losing the formatting it should be trivial to then create a PDF. Or at least that's what the searches indicate.

I wish her luck as it sucks to be stuck at this stage in the process. I know when I was completing my TESL that last term I just wanted out as soon as possible, and she's been at it a few more years than I was.

In Office 2007 you may save your work in PDF without any extensions, this feature is built in the software.

I think you have to install SP1 for Office 2007, though.

Update Office to the latest version (through Windows Update). If it still doesn't have the Save as PDF feature, install the free addon available from Microsoft. Should do the work.

I've been using Bullzip for ages without any problems so I wonder what goes wrong when using it?

If a physical print I comes out ok via printer drivers the output of Bullzip should look the same. Well, in theory, that is.. :)

Also, it's quite a heavy document. To isolate the problem: have you tried printing a single problematic page to see if that changes anything?

Solved, it was a system issue we booted it up on an identical machine and it worked first time I think her window's fonts must of got messed up somewhere.

Thanks to everyone!

ps I'm going to do a give-away in a bit as I do love this community :D

Thank you for suggesting doPdf.
I've been using for years CutePdf but recently I've had issues trying to print from a pdf catalog. I sometimes use it as a quick way to extract just one page from a document.
Luckily doPdf did the work. Now I keep both at hand... :) Thanks again!

You're welcome. Glad I could help. :-)