[Brian]

Hmmmm... I'm actually having trouble reproducing this.

Fired the app up with default preferences - v1.8, current sneaky peek.
Made a new project.
Showed start/due date columns
made "last year/month/week" actions, "yesterday/today/tomorrow" ones, and "next week/month/year" ones.

Used the keyboard to set the start date and due date for each row to the text that corresponded to the title of the action. For all 9 actions, I got 12AM in all the start cells, and 5pm in all the due cells.

Rob, what do you have set for your "default due time" preference. Maybe that's a factor? But if you're getting this in start cells as well, there's something else going on. :-/