Where are you overlap events for your colliders / box? Since you mentioned motion controller I tested in VR as well and was able to use the Set Collision Enabled node to fire my box overlap event when type was set to Collision Enabled (Query and Physics) and skip / ignore the overlap event when it was set to No Collision. Please show where you are using your box collision that it is not being turned off properly.
Also, rather than using the motion controller event, can you replace that with a keyboard button event (such as the T key) and let me know if that has any affect.