I tried it with some other images and it didn't add the extension, so it does seem inconsistent, though I don't see what is causing it.
In the database all of the EXIF and IPTC fields are blank for the images that cause the bug.
I have also disabled all of the metadata options in the admin panel but it still happens.
"File Info" in Photoshop shows no extra data on the images.
Any ideas about what could be causing it?