Need to ease my mind so please answer any advice helpful

ok so I have lost weight several times in the past with no issues but with a lot of factors makes this time different and I never did any weight training before....just watched what I ate n walked the pounds always dropped off...but not now...I have only lost like 3 pounds in the last 2yrs but am finally getting my eating habits that type of thing on track...I have went from a tight 16 to a little tight 12...but when I got with a trainer bout 6months ago she started me weight training which I never did before so I do cardio 3x a week n weights 2x...I almost instantly lost 2in everywhere but I have now gotten it back except for one area im still getting smaller there...so im exactly back where I started she says its because im building muscle under everything...she is very good so I do not doubt what she says but I have this lose fat n skin in my stomach..inner thighs..and on my back under my arms area...will that go away??? and will I start getting smaller again...I do not want to just tone up I want to lose some of it...health problems are keeping me from dropping the pounds as I am goin through pre menopause n my endocrine system is off but ive started some healthy options n it seems to be helping...I was not extremely larger as I know that loose skin n flabby fat is an issue for ppl who lose weight very fast but is it normal for me to have this and is it goin to firm up and burn off???