Sounds to me like something is clobbering bits-n-pieces of your EXIF data or the information is not being properly stored. The biggest trick with lens identification is deciphering which tag is used by OP to retrieve the lens info to match up lens with correct lens module. If you really want to get into this, I'd suggest picking one lens that you're having issues with and play around with EXIF until you find the right tag for that lens. If you're successful, your other Canon lens should be the same tag...hopefully.
If it were me, I'd try to track down why the EXIF lens information isn't being stored properly.