I have a docx Word document, I open it with Word 2008 it has 40 pages some portrait some landscape.When I save as a pdf it saves the two formats separately
so I end up with two lots of portrait pages and two lots of landscape pages.

Can I do anything about this?

How are you saving it? I see two options:

1. File>Save As and choose PDF as the format.
2. From the Print dialog box, click PDF and then select Save as PDF.

Whichever option you are using, try the other one.

EDIT: I saw a third option: From the Print dialog box, click Preview. The document will now open in Preview. From the File menu, choose Save or Save As and go from there.

The Word doc you're trying to convert to PDF probably has section breaks to allow different page setups/orientations within the same doc. If true, I suspect there's little you can do about it, as PDF conversion tries to conserve those orientations, and the only way it can do it is to chop up the doc accordingly. If you could rotate the landscape pages' content to portrait orientation, the problem would likely disappear, but AFAIK Word won't allow that. An alternative could be to do the rotation in a graphics app and import the page(s) as a figure.

Thanks for the suggestions, but no luck, it doesn't seem to want to work.
I can live with it.

If you are willing to put the time and energy into it, you can combine what you have into a single PDF document.

Try the following:
With the master PDF file open in Preview, select Thumbnails from the View menu; you should see a list of page previews next to the main content area. Now you can drag a page's thumbnail from one document to the location of your choosing in the master PDF document and then save the master to have a compiled PDF of all of your [pages].

Excellent suggestion! When I read your post I realized that I had completely overlooked the various PDF merging options out there. In this particular case, it's probably easiest to select all separate PDF files Rain wants to combine and then drop them onto the Preview icon (or double click if you've set Preview to open PDFs by default). They'll open in a single multipage document that you can save. If you select the constituent PDFs in the right sequence, they'll open in that sequence. If the sequence needs adjusting, that can be done by dragging the thumbnails in the sidebar around.

I'm going to recommend Rain to this doc, which provides better instructions than Ira's linked doc (which is really directed towards scanned in PDFs).

Except that the Leopard info is not entirely correct: dragging a PDF there onto the sidebar thumbnail of another PDF opened in Preview does not show a grey double border, but a green copy mark (+) indicating an addition, plus a red line above or below the thumbnail where the added PDF will be inserted.

The Snow Leopard info refers to the insertion point as a blue bar, but the color of the bar is actually that of the selected highlight, where blue is the default.

Thanks for the clarification. (But I don't see an option to change the color of the blue bar in Snowy.)

I figured out how to merge PDFs a while back but couldn't do it again when I needed to recently, and my problem turned out to be that I wasn't dragging one thumbnail on top of the other, which is explained in the doc to which I linked but not in Ira's linked doc.

System Prefs > Appearance > Highlight Color.

Thanks!   I was looking for a pref within Preview.

"For selected text" in the pref you referenced explains why it never occurred to me. (Snowy, at any rate).