Using the regular Media Uploader (since the new one appears mostly broken in this version).
I have several images that 80x80. My Media setting in WP has Thumbnails set to 80x80.
When I attempt to upload an image that is 80x80 the Thumbnail option is grayed out. It only lets me choose full size. Note if I try to upload an image that is 81x81 or anything bigger it does work. Now you will probably say, why dont I just click full size since it would be the same as clicking thumbnail? The reason being is if I click thumbnail it gets assigned as thumbnail class and if I do fullsize it doesn't get assigned that thumbnail class. I need 80x80 images to have the thumbnail class.
So one work around until the bug is fixed would be I could edit the post code after inserting the full version and add the class "size-thumbnail" but on save WordPress removes this and for clients that wouldn't be a real workaround anyway. So currently I have to strech my local images from 80x80 to 81x81, then upload them selecting the thumbnail option which will reduce them back to 80x80 and add the appropriate class.
I know the WP team is working on a new Media Uploader but since that seems extremely far from having even at least the same features as the regular one, I hope this will be resolved. Let me know if you need any other info.
So to conclude when uploading an image the size option should be available if the image you are uploading is bigger or "equal" to your settings in media, not just bigger. And of course is the image you are trying to upload is "smaller" than your media settings, such in my case 79x79 then the thumbnail option should be grayed out.