Alexey, thank you for your response!
After some further testing it appears the 'Active Chunk' masking becomes less accurate with higher numbers of photos in the project.
I tested a project with only 4 photos and all the batch imported masks were clean. With 10 photos, two photos began to show signs of bad edges, and with 30 photos, even more batch imported masks were showing bad edges.
I will send you an email with a link to download a sample project I shot and ran through PhotoScan this morning. I will include all photos and their correctly named background masks, as well as some screen shots of bad edges I got when I ran the project, and the clean edges achieved when reimported for 'Current Photo'.
Let me know if you need anything else!