I just used 9.3.1sp2 and 10.0sp1 to create empty file geodatabases, and the directory
contents are very different (10.0 has nearly double the number of files, most of them
with a ".atx" suffix). What does a 'dir/t' of the *.gdb directory show?
Even if the layout is nominally 9.3, it's still very possible that FTP transfer could have
corrupted the binary files with ASCII translation or a transient transmission error.
- V