ok so its not like she's eating all throughout the day, so she shouldn't be poopin all throughout the day. she's in a small enough crate. and you do take her outside alot. Does she potty on the floor when she was free roam?
The only thing i can sugguest outside of putting her in a ex-pen with a pee pad is to go back to square one and treat her like you just got her with strict food/outside/crate/free roam time. Sylvan explains it best on her site. This is what i did with morgan and she NEVER goes in her crate. read thru it and try it out.
http://sylvanyorkies.com/puppycare.htm the housetraining part is almost half way down the page, but i'd read the rest of the info too because its really good. Stacy always has great information.