I would be surprised to have introduced a PHP error with 1.6.4 (I run it in WordPress debug mode to output all errors, warnings and notices and see nothing), but if any they should show up on your php error log?
I'm working on an API for my other plugin (WP YouTube Lyte), allowing to override default behavior and will probably add something similar to Autoptimize in the future. That future API could allow altering the default behavior as you describe.
To debug this;
- can you confirm you did not have this issue with 1.6.3, or wasn't 1.6.3 active due to the feed-issue?
- can you try if restarting apache changes anything (re my occasional wsod's)?
- can you deactivate all 3 types of Autoptimization (JS, CSS & HTML) and then selectively re-activate them to see when the problem starts occurring?