First you must realize that there are always 2 stories to every situation. If you do not feel free to talk openly with your mother, go out and buy her a card...just a simple I love you card...and write her a heartfelt letter. Tell her what your dad has told you. Tell her that you are not trying to start any trouble, just that this is making your life uncomfortable and knowing, no matter how bad it is...is better than guessing at the worst things. Explain that you are old enough to know what happened and you need to have closure on the subject so you can go on without this stress. Plus you are working for this man that your dad said this happened with so that puts you in an akward situation. If it is true, maybe your mother can talk with the other man and you can be moved to another area at work where you won't ever run into this person. If in the future, you feel it is just too much stress on you...there will be another job in your future, especially if you give your all where you are at now.
I wish you the best and please talk with you mother. It is the longest lasting relationship you will have in your life and I'm sure that you are missing the closness you once had. But as you said, she doesn't even know what is wrong and that is not fair to either of you. If you she knew someone had told you, I'm sure she will be glad to set the record straight for you. Leave the card on her pillow before bedtime ...sometimes it is easier to talk then when all is calm.
Best wishes and I hope you find peace soon.