Thompson,
I so feel for you and the situation you are in. If you check my sig line below you will see that I have stood where you are right now, wondering if he is doing it again, wondering if our marriage would survive this, wondering if he was doing it at all.
I think your gut meter is shouting that you are probably right and that he and this woman are already in an emotional affair, if not a physical affair (and don't bet against that one). The secretive way he "protects" this relationship is way out of line for any man, even more so for an associate minister.
As a minister, your husband is in a precarious situation. I think the devil just salivates over breaking up Godly marriages and if he can bring down a priest, pastor or rabi, well, that's just downright juicy.
Because our pastor has seen so many pastors tempted by affairs and how destructive this is to a church body, he has a rule that he does not counsel women alone, ever. You would not team prayer partners with the opposite sex, either. It is just asking for trouble.
My advice to you is to go right to your senior pastor. Explain was happened in the past and what is happening now. Ask for his/her assistance in determining if there looks to be anything improper going on between your husband and this woman. And ask him to keep it confidential and between the two of you.
Put a key-logger on the computer (if you have one at home), install a tape recorder, whatever you have to do to get evidence either one way or another before you ask your husband again if he is having an affair. There's no point in asking without proof because he'll just deny it.
And lastly put yourself in God's hands to care for you and protect your family, and to give you strength if your hunches turn out to be true.
Hope this helps.
~ Snow