Preview Doesn't Save

I work as a lab instructor and have been having my studets submit papers to me electronically. I will grade them and make annotations so that they can see comments on their writing. This will generally involve leaving a long 'Note' at the end of the paper. from there I will save (I have tried using both Command-S and the mouse menu command), close the file and start working on the next file. I have noticed that many times, preview doesn't actually save the new file. I will open it back up and the file will contain some of the new annotations, but not all of them. I am sure this has something to do with Apple's new "Versioning" and the move away from the "Save As" command (dumb idea), but I don't know how to stop it from happening. I literally just tried saving a file 5 times before closing it, but when I opened it again, no luck. Any thoughts would be welcome, but mainly I hav the dim hope that this complain will get to someone who can fix the bug. Thanks.