Setting it to 1 should make it work like Windows does, but I'm no expert.
This may be relevant:
Quote:
If you plan to set the lower_case_table_names system variable to 1 on Unix, you must first convert your old database and table names to lowercase before stopping mysqld and restarting it with the new variable setting.
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Looking at the database on my Windows box all the tables are lowercase, and it does say that MySQL converts all table names to lowercase on storage and lookup in those docs.