Which version of Illustrator are you using? Seems like I remember something like this, but it was back in version 8-10 or so. It's been a long time, so I can't remember what the cause/solution was.
Does it occur with all files, or just the one you are currently working on? Try creating a brand new doc, save it, close it, then re-open and try to make revisions and re-save. Did it happen again?
Could possibly be a file permission problem, but I don't think so since you were able to save to the original file along with the extra one with the "-01".
Actually, I just solved it. When saving, exporting, etc. I unchecked "Use Artboards" and that fixed it. I think I had it checked because the file I was working on yesterday had two artboards that I needed to export.