Were you using a texture replacer to make the CS water appear blue rather than pink? One problem with streams (of which there are many in the ULs) is that they're often created using animated flowing water meshes, which won't look like water in the CS-generated maps. You'd need to edit them in afterwards if you want them to appear as water does on the rest of the map.
So it seams that streams need hand coloring afterwards.
I think that'll work perfectly.
Anyway, I'm more busy than normal now, but hope to get a working alpha out in not too many days, which can be used by anyone who want to test, and hopefully inspire some to actually create sub-map components.