I have same problem, and found work around:
This work around tested the ability of index services to correctly index a
set of scopes in a catalog by copying the content that
needs to be indexed into a new catalog and clean file tree.
Tested on Server 2003 with all service packs up to date Dec 2006.

1) Use the console plugin for Index Service to Stop catalog
2) Delete catalog entry - confirm all files removed
3) Create an empty parent directory for the content collection and new (4)
subdirectories that will bear different catalog scopes
4) Create a  new catalog entry with a path outside of  parent directory file
path
5) Define  the top level sub directories in the index services console for
the 4 scopes needed
6) Start indexing service.   Docs indexed is 9 which is the count of the
directory tree nodes so far, so good
7) Copy content into the first two scopes and check the results. Total docs
moves to 22, and matches the entries in the catalog directory hidden
00000002.ps2 file.  The Index Service query form works correctly. OK
8) Copy a larger number of documents and subfolders into the third scope.
File counts and query OK
9) Copy a significant number of files into the fourth scope. Total docs rise
to 1041 and matches in  00000002.ps2 file OK
10) Add an exclude scope to the existing first scope which eliminates one
file. OK.
11) Add an exclude scope to the existing fourth scope with eliminates 17
files and folders. OK
12) Delete a file in an existing scope.  Total docs does not immediately
change.
13) Delete a large subtree in an existing scope. Total docs drops
immediately and matches ps2 file. OK
14) Copy a large subtree into an existing scope. OK.
15) Add a directory in the file system and add a NEW SCOPE to the catalog of
485 items.  Copy in three files and Totals change to 488 which matches in th
e
ps2 fiile.
BUT the new path names appear out of place in the PS2 file.
Instead of being added to the end of the PS2 file as previous entries and
changes, the new scope paths are intermixed with the files in the last scope
accessed.  Everything still appears to work OK. This may or may not be a
problem.
16) Add a directory and  ANOTHER NEW SCOPE 6.  Copy a large number of files
into the scope 6 scope and it apperars to be OK.
17) Add 10 files to the scope 5 area. OK
18) Merge the catalog just for grins. OK
When the above manipulations are complete the status of the catalog is 624
total documents.
19) Now delete the catalog and add back the above scopes in a new catalog
and start the service.
Only 527 of the 624 prior files are found by the index service.
And that proves the problem and the work around.

[ Post a follow-up to this message ]