UPDATE: See this article for latest status
If you upload a file with the same name as a file that was on the file cabinet page before the new file uploader was introduced and the name of that file contains spaces then it creates a new file rather than creating a new version. Subsequent uploads do then generate new versions but for users relying on versioning this is clearly a problem.
(What appears to have been happening is that previously blank spaces were stripped from the attachment names. As of 25th Jan it appears that blank spaces were not stripped. However my tests today (28th Jan) indicate that behaviour has reverted to the previous functionality and that blank spaces are being stripped again)