From my testing, this is what counts towards IGT:
- Cutscenes
- Deaths/restart checkpoints (so it's not like GoW1 where if you die the igt resets to what it was before)
- Portals
- Shops

This is what does not count towards IGT:
- Loads
- Pause menu (pressing the options button)
- Weapons/map menu (pressing the touchpad)

Another important thing to consider: IGT starts counting on the main menu, before starting a new game! So when starting a run, you should open a savefile, and, when ready, rush through the menu as quick as possible after quitting the current save.