Have you considered putting another litter boxoutside her cage in the area where she runs? It could be she just hastoo much freedom and is forgetting to go back to her cage to do herbusiness.
You are doing the right thing when you pick up the stray poops and putthem in the litter box. As Spring suggested, you can also wipe up anypee with a paper towel and throw that in her box as well. This isshowing her thats where it goes
Also, does she have hay in her litter box? I like to put a little bitof hay in one corner to encourage the bunny to go in there.