Spotlight gives incomplete results in Mountain Lion

Hello. Since I use Mountain Lion, Spotlight gives me incomplete results.

-- I already cleared all the relevant caches

-- I already asked (in fact, several times) to rebuild the index

-- I already rebooted.

-- I already verified the disk, repaired permissions, and done all the ritual things.

No matter what, Spotlight misses files (both in searching by content and in searching by name) which are in the computer. I can see them in front of my eyes in one finder window, but if I open another window and spotlight for the name of that file, I get no results.

When I look at the console messages, I do find errors by mdutil, but they do not seem to be connected with the files that do not show up. The errorrs are of three kinds:

-- one concerns separators

9/5/12 12:05:47.973 PM mdworker[8924]: No separator between the header and body in message <_CMFMemoryMessage: 0x7f8fea462f40>

(this concerns emails)

--- another is a write error given by sandbox:

9/5/12 12:30:36.294 PM sandboxd[9129]: ([9128]) mdworker(9128) deny file-write-owner /Users/luca/Library/Containers/com.apple.Notes/Data/Library/Notes/NotesV1.store data-wal (import fstype:hfs fsflag:480D000 flags:40000005F diag:0 uti:com.apple.notes.externalrecord plugin:/Library/Spotlight/Notes.mdimporter - find suspect file using: sudo mdutil -t 11694802)

(this is a funny one, but it does not concern the files in question. Incidentally, the mdutil manual does not report a -t option for what I can see)

-- a third one is an EOF error but not one that helps much in understanding what is what:

9/5/12 12:31:23.596 PM mdworker[9105]: Unexpected EOF, returning last token as fallback

Now, what I do not know is if such messages may in any way influence the way spotlight works on *other* files, maybe blocking the full indexing of the disk or something.

Any suggestions?

Thanks,

l.