I've had the same problem in various versions of Illustrator on the Mac, up to and including CS3. Based on the previous comment, this appears to happen only if your Illustrator document starts life as a generic PDF file. So this is my solution (which worked today for me).
- Make sure all layers are visible and unlocked.
- Copy all your artwork to the clipboard (Select -> All then Edit -> Copy, or cmd-A then cmd-C)
- Create a new document with the same dimensions as your original one.
- Show the layers palette, and choose "Paste Remembers Layers" from the popup menu.
- Paste your artwork into the new document (Edit -> Paste or cmd-V)
- Save the new document.
You should be able to edit and re-save the new document whenever needed after that, although you may find that the file is larger than the original one.