OK thanks. As I'm writing this version 4.0.3 is being pushed out and will be in the repository in a few seconds and will show up as a new version within an hour.
It contains a checkbox under scanning which enables "high sensitivity" scans. This reenables this feature, but we search for eval( with a parentheses on the end along with the other functions. It's off by default, but it's there if you're doing a site cleaning or some other activity that needs high sensitivity.
I'm marking this resolved in a few minutes unless anyone has any objections.
Regards,
Mark.