In the words of the song: "How long has this been going on?"
Have you recently upgraded your original Outlook Express - which would have been Version 4 - to Version 5, or higher? The e-mail formatting is slighly different. This fact is normally not noticed until you try to import an e-mail into Version 5 that you have exported from Version 4 as an "eml" file.
What was the last action you did to the system before this problem reared its ugly head?
One thing is certain, your e-mails are intact and there is no reason to lose them. There is no limit to the size of the Inbox that I know of. I have seen over 2000 e-mails in my inbox. Such a large inbox just slows down the speed of loading of OE when you open it.