> this morning the live version menuing stopped working.
> Only difference between live, staging and development servers is ....
1. Real Staging servers use the same (or closest possible) setup as Live.
2. Computers are automatons - if their behaviour changes it's because they were told to change. If the software doesn't differentiate between environments or yesterday then something else changed - so the poor server setup is not the only difference, and your first step is to identify which other differences exist.
> If I put a copy into a subdirectory on the live site, it works, cookies and all.
Check your version control history for what changes were made - sounds possible that somebody may have set/changed the path attribute of the cookies. Then again, you would have spotted that when you compared the actual cookies for the different environments to check for differences, so maybe it's something else.
EDITED: 25 Jul 2015 15:45 by BOUGHTONP