The difference is the depth of comprehension one can reach.
While active in the physical body, we do not have the senses to see the roots of the defect, which are not physical but in the internal worlds.
In meditation, one can (with skill and development) see into those worlds in order to comprehend the defect completely. Without in depth comprehension (deep understanding), the defect will remain, awaiting its chance to feed.
"Do not worry; cultivate the habit of being happy." - Samael Aun Weor