There's a type of personality aspect called the "Conflict Avoider". This may be her. If so, pay good attention to what I'm going to tell you.
You see, those types claim on the surface that they agree "for harmony's sake". They want to "make everyone happy", they say. They want to "keep the peace". They may (erroneously) believe that not having any disagreements makes for a happier relationship.
The truth is, they have an inward fear of asserting themselves. They would rather lie then be honest with you. It's as if they're scared you wouldn't be able to "work" with them if they opened up to you. Or, if you have a history of losing your temper and yelling and/or verbally, emotionally or physically abusing them, they'll keep quiet as well. I'm trusting it's not the latter in your case, though her lowered self esteem makes me question what's been going on in your relationship. Do you show her your annoyance with her? Do you argue that her viewpoint is wrong? Do you belittle, dismiss or discount her feelings or views on matters because you think she's got it wrong? Do you feel you're always right? When you have arguments and conflict does it mean acting in an angry or mean fashion? These are all a matter of learning better how to resolve conflicts agreeably. Just covering the possibilities.
Suffice it to say that what happens very typically with these "avoider" types is that, though they appear to have agreed on the outside, inside, they are angry. They feel like they never get their way. This anger, because it's directed inward, is very damaging, and leads to depression. Very often, just about every time, conflict avoidance is a precursor to the relationship breaking up, as that anger, frustration and resentment build.
You're going to have to lead her through this. When she agrees so readily, YOU have to not let her. "Honey, I get the feeling that, even though you've just agreed, it's not really where your heart is?" Listen to your gut here to suss out how she really feels. Get her to open up. Show her that it's safe to do so. Don't attack her viewpoints, even if you don't agree with them. You don't have to agree with them, you just have to put yourself in her shoes for a moment and UNDERSTAND them.
Everyone's entitled to their views, even if they're wrong. And her feelings? Those she's entitled to, and there is no argument that she can't feel however she wishes to feel. That's her stuff. Just listen and understand without judgment or interruption. That's what she needs from you.
Once you get where she's coming from, even if it's off the wall to you, remember that it's a big world, and not everyone sees things the same way, and yet, it has to work out somehow. So the way to work it out is to reach a TRUE compromise.
Now, a true compromise is NOT: "We'll do my way this time, and then next time, we'll do what you want" or "We'll do it your way this time but next time we'll do what I want". Someone always feels that they lost and that the other person won when that happens. That doesn't stop resentment from building.
A TRUE compromise has to be a win-win situation. That's the goal in resolving any conflicts.
Hope this helps.