What a miserable spot for you to be in! It is terrible for you to know something isn’t right but to be stuck in how to move through it. There are lots of different ways to approach this, so keep in mind that my advice is just one avenue.
I would talk to your mom and tell her what your thoughts and feelings are about how her behavior is affecting you. Don’t assume, accuse or blame, but rather give her feedback about how her behavior is affecting you. (“When I come over and you run off to the computer or leave the house on an errand it makes me feel upset because you seem so distant.”) Explain that it seems she is distracted and not focused on the family and that it gives you cause for concern. Let her know this isn’t something that has happened once or twice, but you have been feeling this way about her behavior for a while.
This allows you to stay focused on what is real between the two of you without going down the path of accusation. If your mother is having an affair – which it sounds like she is, an emotional one at least — these tend to end badly for everyone. The chances are that your father has noticed the change in her behavior and they will have to deal with the eventual conflict. Stay focused on your relationship and how her behavior affects you. This will keep everything on the table as to the dynamics of her relationship with you. It gives you the chance to say something about your discomfort, and may give your mother a wakeup call that her (not-so-secretive) behavior is affecting others.