Most Apps on 2nd HDD - constant flags and warnings when I use them


I have a small SSD for my OS (Win7).
I intentionally install most apps on my 2nd (D:) drive.

Comomdo is dimming my desktop and throwing up warnings every time I do anything
including “Email this link” because Thunderbird is on the “D” drive.
Making many operations take far too long.

How can I tell it to ignore the program files folder on “D:” ?