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The first thing I'd do is to check the master page for a white box. If you didn't create the ID file yourself, and if you have any text on the master page, click into the text frame(s) with the Type tool and go to Edit>Edit in Story Editor, and look for an anchor (indicating the box is anchored in the text, as opposed to being a free-standing white box). If so, delete the anchor with the type tool the way you delete a text character.
Cheers for the responses guys. I'll try them out and report back!
Turns out it was an issue with the images that i'd put in (not 100% sure what!). I don't think it was on the master sheet as I left that alone, but took out the JPGs in the rest of the document and put them back one by one. Can't say what was causing the issue before because I set all the transparency settings the same and placed the images in like before, but at least it's fixed now!
Update: It would appear it happens when I print the PDF as an image. /facepalm....
Thanks again for the replies and help