Sorry for the late reply, as this is an older discussion and you still seem to suffer the same anomaly.
If you have two DSC's that service the same domains, you should cluster them. Otherwise both DSC's will respond to all ID queries and you'll get double assignments.
DSC's can be clustered by not defining them in System->Setup->Directory Services Connectors (green + icon), but by removing one of the unclustered DSC's, going one level down to the tree entry of the remaining DSC and clicking the green + icon in the General tab under "Cluster". You can change the name value to reflect that you have a cluster instead of a single DSC with a specific machine name.
The advantage of clustering DSCs (aside from not getting double CAL assignments anymore ) is that your domain queries will become resilient (one DSC can go down) and the load is distributed.
Note that you don't need a cluster license to do this.
[Edit] Corrected a lot of spelling errors. I seem to be getting worse at using keyboards :-(