> Anyone know what might be causing these

"Trying to (re)create a formatted document by converting a .pdf" is my guess; not really the workflow .pdf was designed for, and all the more problematic when you're trying to move layout/formatting between programs that handle them very differently. I'd extract just the text from your IDD files and then redevelop the required layout in Word. The story editor is a relatively painless route to export, if some way from ideal for this particular task :-}

btw, scouting around in the IDD forum turned up the suggestion "use the script ExportAllStories.jsx that comes with your default InDesign installation" – no sign of any scripts in my CS5 IDD, unfortunately, but you may be luckier.