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The script includes a CFunction named Include which uses luaL_loadfile()
to load chunks into the same lua state.

If I understand correctly your main script loads other scripts using your own Include function, now based on luaL_loadfile.

Are you sure this Include function also _executes_ the scripts that it loads?

If you changed the old lua_dofile calls here to luaL_loadfile ones, this isn't the case...  [and you'll have to make sure the chunks are actually run, like you do in your main routine]

Sorry if I'm stating the obvious: it's tricky to keep track of changes to someone else's code at a distance [;-)].

Ashwin.
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