Have you tried starting over from scratch with just the rawdem, agreestream and innerwall data? I did this recently and it helped be get past some unknowable problem that was hanging up the AdjointCatchment creation process. My view of it is that starting from scratch makes sure there isn't some residual setting or variable that is hindering the process.
If you put the new mxd in the same directory, it is good to give the data frame a different name so that the folder and dataset names don't conflict with the old ones. To avoid this hassle, I will often close Arc Map and using Windows Explorer delete the folder with the rasters and the geodatabase created by Arc Hydro. These are all recreated when you run Arc Hydro tools. The only layers I save are rawdem, agreestream, innerwalls and outerwalls (not used much). I will also often save the batch points if I set them manually since is can take time to set them in the right place again. If you copy the batch points in the save batch point layer to the new geodatabase for the file and data frame, you have to set the "BatchDone" value back to 0 so the batch watershed or subwatershed delineation tools will work.
Hope this helps.
