For a quick fix, and since it sounds like you're using notepad anyway, try cutting and pasting the content from Outlook into a notepad file. Don't just drag the e-mails, open them, select all (to highlight all the text), do a copy, open a blank notepad file, paste the text, then save it where you want it. Outlook e-mails sometimes act strangely once they're moved outside of Outlook (Outlook express is particularly problematic).
Can you give more information? Maybe a step-by-step walkthrough of what you're doing? I'm not sure I completely understand what's happening.