Failed wordpress 3.0 upgrades

A client recently attempted to upgrade their site to WordPress 3.0 (they were on 2.9.2. It failed and they received an error like the one blow

function.require]: failed to open stream: No such file or directory in /home/username/public_html/wp-settings.php on line 19

Fatal error: require() [function.require]: Failed opening required ‘/home/username/public_html/wp-includes/load.php’ (include_path=’.:/usr/lib/php:/usr/local/lib/php’) in /home/username/public_html/wp-settings.php on line 19

We have since tried another auto upgrade and a manual upgrade with the same result. I copied the site to a seperate location (on the same domain) and upgraded that – and it worked perfectly. Strangely when I copied this back to the actual location and changed the url in the database it immediately produced the same error message above.

Can anyone offer any suggestions as to where I may find the answers to this puzzle?