Preferences change when loading different project..?!?

Hi, I though Preferences are global, and not project dependent. Or they should be, so this must be some kind of bug.

In the VST section of preferences, there is something called “mute pre send when muting channel” that you can tick. I have it unticked for silent side-chain sends. So, when I save the project and restart and load Cubase, if I first load my default Template, my setting is correct(unticked). If I then load the saved project with the silent side chain sends, the preference is ticked, and the silent send is nonfunctional and I need to go in to the preferences and change it. every time.

Weird huh?

7.5.1, OSX mavericks