I agree with both posts above....having been in a LDR, it is very easy to build up a fantasy about the person that sometimes doesn't live up to the reality. In my case, it had more to do with realizing my ex had so many issues, I knew making it permenant would be a horrible mistake.
The thing is, it seems you've been letting her run the relationship from the beginning in one way or another (she started it, she wanted to skype, she started seeing her ex again which caused your emotions to change subtly from 'really like her' to 'really can't trust her' , then back to 'really like her' etc.) ...basically you've kinda just been along for the ride. Eventually, your mind or heart or both is going to rebel, when it finds its trapped in a relationship you really weren't prepared for, with someone you may 'like' but who actually annoys the h*ll out of you. And take my word for it, if the little things are annoying you now, they will just get worse over time.
My advice, for what it's worth, is make a list of all the things you 'really like' about her, and all the things you don't....all the reasons you should stay (or get back) with her and comparative reasons you shouldn't. Be as objective as you can. I'm pretty sure you'll know what to do when you're finished.
Of course, I'm pretty sure you already know what to do. If you need permission, don't expect it from her. Expect it from you....forgive yourself, and her...and let go.
Take care