Spotlight indexes wrong HD Mac Mini Server, OSX Server 10.6.8, dual drive

I cloned the first hard disk (HD1) to HD2 using CCC, thus creating a bootable copy.
However, now I discover that when I startup from HD2, Spotlight has been indexing only HD1.

Using a Terminal command to rebuild the Spotlight index doesn't help. 
I get the message for HD2: There is no index.
Using the option for all volumes, it only rebuilds for HD1.

This problem is nasty, as I intend to use an Automator script that filters files, and for this it uses Spotlight (I get an error now).

Any ideas how to bring OSX to build an index for HD2?
mdutil -s /Volumes/* will show you the indexing status of all available volumes.

mdutil -i on /Volumes/HD2;mdutil -i off /Volumes/HD1 should do what you're asking for.  might need to sudo based on ownership settings of each.