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While researching stages of meditation, I came across something which could shed some light on your experience. In a section covering Khanika Samadhi (momentary concentration) I found a similar description of your experience. While the author is writing specifically about the noting technique in Vipassnana, I think technically it has relevance to Goenka scanning as well.
Pure Vipassana yogis can appreciate and understand the power of Khanika concentration. For when their noting gains momentum, they can see for themselves how the noting goes on by itself uninterruptedly without a break. The noting seems to run on its own steam without any need for the yogi to make any concerted or deliberate effort. Thus, it is not unusual for a yogi to be able to sit for an hour, and even several hours, absorbed in noting. During good noting, especially at the insight knowledge of equanimity (sankhara-upekkhaΓ±ana), the mind just stays put on its objects and refuses to wander. Even if one wants to send the mind out, it refuses to go and it recoils back to whatever Vipassana object it is noting.
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This automatic body scanning that you mentioned is your ego playing games with you. During meditation, your Self or ego is becoming weaker and weaker. When the ego sees he is dying, ego will do everything to not die. You could hear sounds, vibrations, gain supernatural powers, travel to distant galaxies, predict the future, read minds, gain magical powers, fly through walls, visit astral planes, talk with devas, have out of body experiences, etc.
Ego wants you to cling onto something. Ego wants you to crave. That's why he gives you weird experiences. If you show fear to such experiences, ego will give you experiences that you'll be afraid off. If you show attachment to such experiences, ego will give you experiences that you'll be attached to.
The important thing is not to get attached to these experiences and get beyond them. Don't worry, if the experience arises, just go with it, enjoy, relax, have fun and don't intellectualize. The most important thing: never, ever be afraid. If a bad experience arises, smile, don't worry, just go with it, enjoy, relax, have fun and don't intellectualize.
The closer you will be to liberation, the less such experiences will arise.