I promised I would talk to the developers, and I have (inukshuk, who replied above, is our lead developer 
). He and I discussed this at length this morning. We agree that there is some work to be done here. The easiest fix is coming very soon, when we make available a “Date added” column. This column will allow you to sort all your materials by when you imported them. Then if you sort by that column, your stuff shouldn’t reshuffle.
Hashing this out also led me to a slightly new workflow, which I’ll probably write up on the blog once the new columns are available. The tl;dr version is that it might be easiest to work with the Last Import list (it appears in the lefthand pane) to process through your items initially, because there will be fewer items to work with and so it’s easier to see them even once some of the metadata has changed.
Thanks for bringing these things up–you definitely sparked a conversation that we needed to have!