Sorry to tell you this Buster, but anything your wife tells you that sounds truthful isn't worth a crap. She's lied to you twice now and took him over there...
My wife keeps telling me she's "just checking email" and I can look on the network and see if she's on her second life website talking to him or not...and most of the time she is talking to him. Often times when they tell you they are respecting your feelings its BS and just a smokescreen.
She MAY be keeping the OM away from your home, but its not for your feelings, its because you have surprised them twice and they likley dont' feel safe there anymore.
Are you telling her what your work schedule is? DONT.
AGAIN : Why are you talking to her? DETACH.
She violated your marital home, SHOW her it pissed you off and what happens when she does this. She did this and you just talk to her and enable her to continue by not showing the damage she's done. END CONTACT with her to show her you don't approve.
Get someone else to exchange your son. You need to get a middle person to represent you so you can distance yourself man. You are NOT following advice here.