My old hack should no longer be necessary as of 0.9.6.1. Sirlancelot implemented a new fix using REPLACE INTO queries instead of just disabling the JavaScript. The bug report can be found
here.
I wonder if perhaps your MySQL user doesn’t have enough privileges to run REPLACE INTO queries? Does that user have full admin privileges, or something lesser? There are some other issues specific to REPLACE INTO syntax which might be useful and can be found
here.
I can’t replicate this issue on any 0.9.6.1 installation that I have now (MySQL 4 or 5), so it’s tough to debug.