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I am not absolutely sure what your specific question is, other than support and some direction.
I am going to suggest to you that the reason your wife may have issues that appear to come from no-where may be linked back to the abusive and violent background that she endured as a child. When we experience a highly emotive situation, the subconscious mind can absorb beliefs about the world and about ourselves that lie within the subconscious mind for many years. We are often unaware of them, or squash them down if they surface - they they re-surface many years later in anxieties and worries. These beliefs always have the role of protecting us (for example, I am not safe to fly in an aeroplane) although it appears irrational, it's purpose is good. Your wife may have family/marital/safety beliefs going on for her that she genuinely doesn't understand, but feels strongly that she needs to respond to (by leaving). Out of the marital home, her 'triggers' may be less obvious and she may feel more comfortable and confident in her feelings for you, so she returns. Then the 'marital situation' re triggers her fears, so she becomes argumentative and leaves, thus creating a cycle, leaving you wondering what on earth you have done wrong.
It would probably be very effective for your wife to see an EMDR therapist, who could help her to unravel and let go of the irrational and destructive beliefs that she may still be holding from childhood. Consciously, she is probably unaware of them and unable to discuss them. The therapy is all done in the subconscious mind and can therefore be relatively quicker than talking therapies and can allow clients to view their world without the distortions. Have a look on the website www.emdr.com for more information and a local therapist. Obviously your wife would need to be in agreement to go. It is a trauma therapy - which is exactly what a violent and abusive environment is to a young child.
I hope this helps, Best Wishes, Sarah