Setting the framerate mode is not a suitable mechanism to implement pausing. Either use framerate independent mode and it happens automatically, or disable the behaviors when pausing. If you think there is still a problem when not changing the framerate mode at runtime please make a new report.
1) The documentation says that the Framerate Independent mode isn't as accurate as the other mode. How much difference do think it really makes?
2) Disabling the physics behavior doesn't work (I tried it) because for example if the player, which has the physics behavior, is in the middle of a jump and I disable the behavior to pause ... when I unpause and re-enable it then the player just drops straight down instead of completing the jump. If I flip from Fixed to Frame independent mode when I pause and then back again when I unpause then the physics calculations continue where it left off when I paused and player completes the jump.
I am "tricking" C2 into freezing only the player, enemies, moving platforms, and other "play time" game elements (even physics behavior objects), yet still allow full C2 functionality during the "pause" for the game menus, dialogs, etc... I have tried all kinds of different ways to do it without causing some negative side effect (like #2 above), but the only way that works is 1) Disable Sine behaviors, 2) Set ALL physics objects to "Framerate Independent" and time scale to 0, and 3) disabling all events directly related to updating "play time" objects.