We have made some changes that require us to disable and then reenable the entire transform hierarchy whenever we replace a Transform with a RectTransform. This has created the undesirable side effect of calling OnDisable/OnEnable on all scripts attached to the hierarchy. This is a behaviour that we intend to address in the future.

There is a simple workaround for this though. The problem is caused by when we swap the transform, so a simple solution is to add a RectTransform or UI element to the GameObject on creation so that the swap does not need to be performed.

For example
var go = new GameObject("Canvas", typeof(RectTransform));