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Were you using an image stabilising lens?
I have had a similar effect when doing a time lapse and forgetting to turn off IS. Some images were shifted just slightly - the ones where the lens IS obviously kicked in. All shifted by the same amount. The affected images weren't in an exact pattern like you explain though.
Maybe every second pic the lens detected slight tremor from the mirror/shutter or something and IS activated.
But if stabilisation was turned off my whole theory is nonsense!
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