When I had that feeling I checked BF's work email and found that he had attempted to delete a flirtatious email conversation with a contractor he used to work with. I woke him up and confronted him immediately. Maybe not the best timing but I knew I wouldn't be able to sleep and my anger and resentment would just grow overnight.
He admitted to deleting it because he knew I was checking his email and realized that it didn't look good. His explanation was that he was just being friendly in order to maintain the business connection (if he ever went into consulting she works for the company he would want to work for). He didn't realize how it looked until several messages in and then panicked about how it would look to me.
I was beyond furious. I had told him before that even the appearance of infidelity would be enough to send me packing. And to top it all off this happened the day before we were to host a party at our house for all of his department.
I do recommend being as calm as possible (I wasn't, definitely could have done better with that) but do speak up and ask him about it. Waiting too long will just let you stew and build up more anger and resentment. Try your best to listen with an open mind. When he is done with his explanation trust your gut instinct as to whether or not to believe him.
If you love somebody, set them free. http://tinyurl.com/2empx2g