You know, symptoms like this can have so many causes. If it were me, I would try to eliminate any possible causes of bacterial infection. Letting them eat off the floor is an obvious one. Also, if a bag of their food lasts a while, humidity could be getting to it, allowing for bacterial growth. If that's the case, a good storage container would help.
There was a thread recently where the poster had an issue with bloody poop. I had been through the same thing with mine so told what my circumstances were. I was able to eliminate the problem once I figured out what was going on. While it was happening, I rested my dogs' stomachs and gave them kaopectate. It worked well for the immediate symptoms, but didn't fix the problem until I found the source. Here's the link to the thread....
http://www.yorkietalk.com/forums/sic...oody-poop.html
Everyone's situation is different, so there's no one size fits all answer, but you have already posted about a couple of things that could be the source. Best of luck in getting to the bottom of this.