Hi and thank you for that information. Boxers are prone colitis so make sure to have her examined and make sure there is nothing health wise going on especially if this problem began suddenly or if its been a problem since you rescued her. Dogs that are brought to rescues or pounds especially purebred dogs, may have initially come from a pet store and if that is the case then the dog was 99.9% bred in a puppy mill. When pups are born in puppy mills or with back yard breeders, the pups usually have or develop many health problems. This is why as a trainer I always suggest possible heath problems be addressed first.
As well coming from a shelter has taught her to eat and sleep near her own eliminations which most dogs do not like to do. Shelters are great but they have limited staff that cannot go in and clean up as soon as the dog has an accident. I find shelter dogs to be the longest to retrain in the potty area.
If this is happening when you are not at home or when the dog is separated from you, then you may be looking at separation anxiety (SA) and steps must be taken to address that issue. http://www.wagntrain.com/SeparationAnx.htm
Some dogs do panic in crates and panic more with SA , so if it is being put in a crate that upsets her then try keeping her on a tether and eye bolt next to her bed and bowl of water. Just be sure she has a flat buckle or snap collar on and no training device such as a choke chain and do this for a few days when you are home to gage her reaction to it.
If you work she may need more frequent outings as well so having someone take her for a walk or just let her out in the lunch hour may help.