defecating in crate

Hi. I have within the last month rescued a second JRT from the local SCPA. The new one is a 2year old neutered male. When I first got Fred, I let him loose in the house while I was away. I have STOPPED that now because he urinates, defecates and chews on things in the house. Fred likes his crate and will willingly go into it. The problem, however, is that when i get home from work (approx. 5-6 hours later) he has defecated in the crate. I take him and my other JRT for as long a walk in the morning as I can (about 20 min) and this is the time the other does his business. Fred however doesn't seem to get a handle on the fact that this is the time to go. He also doesn't go when we go on a longer walk after I get home. I've begun to dread coming home because I have to constantly clean up the crate (which btw, is more liek a pet porter.... it is large enough for him to move in but not too large that he can only be in one part). Any ideas? I really love Fred and when I'm home on the weekends... he is fine.