Hi David,
with 15,000 tables you are talking about a LOT of files to hold these (30,000 files with one index each and each database being small enough to not need more then one file to hold it), on linux ext2/3 this many files in one directory will slow you down horribly.
We use ReiserFS, and I don't think that this is causing the problem ... although it would probably help to split the directory up using tablespaces.
But thanks for the suggestion!
