I found the cause to this problem: When editing an entry, the user is able to change the file uploaded, but the new file does not show (file is not linked to in the entry) and his upload allowance is not updated.
This bug persists if you installed LDM's extra swfuploader plugin (problem described in my previous post). If you use the default uploader, this problem does not appear. Solution: disable/ uninstall the swfuploader until that plugin is fixed.
Andrew, can you please patch the swfuploader 'cause having the progress bar is really useful? Otherwise, please provide an option to disable changing the file upload when editing an entry.