Ever since Akisment 2.5 was released, I've had problems on several WordPress installations with it marking normal comments as spam.
Disabling Akismet will stop it, but I really don't see that as a solution.
I'm about ready to go back to 2.4x.
The following plugins are installed:
Comment Timeout 2.1.1
Login Lockdown 1.5
My Custom Widgets 2.0.5
Creative commons license widget 0.7
WordPress version is 3.0.4