Thanks for the tips. I did make adjustments before saving from DSS. I figured at 16-bit it'd preserve more dynamic range if I stretched out the values some. Otherwise the images look very dark. But I'll heed your advice, Bojan. Thanks!
I did not use raw with DSS but tiff converted from raw with dcraw. The reason for that is to cut down on DSS' workload. (That way I can also reduce the size of the images before feeding them to DSS. I only have a Linux PC, and DSS won't run in Wine, so I've been using my spouse's Win7 laptop when she's not using it. It's not a particularly powerful machine. I already got one out-of-memory error with the 4GB RAM it has.)
In the long run I hope to get away from DSS and do all the processing with lower level tools, but as it's early days I'd prefer to see some results and want to understand all the steps before I go full-on nerdtard with the processing.