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I'm with Mish on this one, I think you need to address the problem asap.
You still have her, she still feels for you and knows shes in a committed relationship with you. Her actions are not excusable, what she has been doing is wrong and emotionally she is cheating. I think that Mark's wife has every right to know whats going on too. Shes in a committed relationship and would want to know just as much as you would if something was going on.
If you let this fester you will lose her or you will fall into an unhappy marriage. Tackle the problem while you have some fresh firepower and before she checks out anymore than she has.
Look, you snooped in her in box, but at the same time you should have never had a reason to, she gave you that. Generally if you think theres something going on, then more than likely there is. You're in a tough spot but you're a smart guy.
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I also have no respect for someone that has these doubts and issues with a relationship and won't speak on them. She will wait until she can't take it any longer but by then it will be too late and the marriage will be doomed.
Now is the time to act.
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Everyone's advice here has been good.
All I can say is this: these emails are testing the boundaries. She's poking to see how he will respond. As long as he stays aloof, maybe nothing will happen. However, if something should happen between them that would push them past these thin boundaries they've set up, it sounds like your wife may have an issue with restraining herself. This is dangerous stuff, my friend. It needs to be addressed immediatly. Take it from someone who's been there and unfortunately had a bad end result.
Regards of it being 'flirtatious' emails, it's called emotional cheating. Not acceptable. This is still a violation of your relationship and you need to take it seriously. Yes, you snooped, but I think you need to own up to it and confront her.....in the mildest way you can think of.