Are you asking if what you observed and she then said about having sex with her boss in a very submissive-role-playing way is REALLY true or only true in her fantasy? And you have said that she is very submissive in sexual encounters with you, so it seems possible that she is so enraptured with the dom/sub sexual entrancement that she doesn't have any energy for sexual relations with you unless you play into the dominating role she wants to react to. The dom/sub scripting for sexual relations is a high-emotion+erotic stimulation form of pair masturbation that falls flat if both people aren't oriented to playing their roles according to rules that haven't been worked out together. Are you saying SHE said SHE was selfish to want to act out her sub-role with the boss who was up for acting out the dom, or was she excusing herself by saying YOU were selfish?
If she was admitting SHE was selfish, then she could be willing to face the hold that compulsive dom/sub sexual acting out has over her, and you could go to a sex therapist to try to develop your own sexual life into something more spontaneous and perhaps even romantic--IF that's what you want. What do you really want in this relationship with her? You are in the 3rd year of your relationship, which is usually about as long as a romantic & sexually intense relationship lasts. So it's a natural crisis time for any love relationship, whether married or not. So she may have been sufficiently thrilled erotically with allowing your desires and actions to dominate, but not actually being able to find herself in the partnership--and this crisis she has created by cheating may be an unconscious way of trying to find a more real way for HER to be in relationship, which is also an invitation to YOU to find more spontaneous and personal ways for you to be in this relationship. Your ages and your intentions in this relationship could matter now, as you react to this shattering of the way you were up to now. What do you have in common with your partner outside of your sexual relationship that could reward you for continuing this relationship? And do your want to continuing sexual habits of domination and submissiveness for the excitement they bring? Or do you want to reach beyond to find more personal expressions of love along with the sexual habits that have carried you this far?
I think her embarrassment (covering her mouth) was proof of honesty and remorse; so she really does want to have an authentic relationship with you--and she may well realize that the dom/sub sexual compulsions are a burden that may be sabotaging her freedom to have a chance at a more personal & unique love experience with you.
Let me know if some of this makes sense to you, since I'm not entirely sure how well I understand the experience you have been having with her for these 3 years. But "submissive but stubborn" suggests to me that she's stuck on particular ways she's in the habit of being treated as a submissive partner, and you may be trying to play that role of dominator as well as it feels to you to do so, but not actually as compulsive about the dom moves as she is about the sub moves.