Peeing and pooping in the house & crate, Please Help?

I rescued a chihuahua in December 2010. She was 2 when I got her. Crate issue - When I am not home I create her and my other big dog (in separate crates). Before crating them I always make sure to let them out to use the bathroom. Most times when I get home she has either peed or pooped in her crate. This... show more I rescued a chihuahua in December 2010. She was 2 when I got her.

Crate issue - When I am not home I create her and my other big dog (in separate crates). Before crating them I always make sure to let them out to use the bathroom. Most times when I get home she has either peed or pooped in her crate. This occurs when I am gone anywhere from 15 minutes to a couple of hours. I made sure to get her a small crate, going by what I heard that they won't sit or lay in pee or poop. Not this case she will sit\lay in it. I have to bathe her often because of this.

House issue - I let her out about every 2 hours when I am home. I figure she has a smaller bladder than my 70 lb. dog and needs to go out more often. She uses the bathroom outside most times. But sometimes I will let her in and 5 minutes later she will go in the house. She is very inconsistent about the times she does this, the place, etc. At first I thought it was because she did not like the cold (I live in CO). So I made sure to dress her if it was snowing out or if there was snow on the ground (jacket and booties to cover her feet). I made it through the winter with several accidents. Now it is spring, and still we are having issues, not nearly as many but still a few.

Things I have tried:
Puppy Pads

Waiting longer when I let her outside before allowing her to come in (my bog dog just goes out and does his business then comes in, with her I leave her out there for a bit)

Different crates (I had more of an enclosed one when I first got her similar to one you would travel with. Then I switched to a more open one made of black wire)

Praise and cookies when she does go out side

I need some help.
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