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I've been desperately trying to track down a problem that arose while working on Nmap's scripting engine. I had a userdata that I pushed onto the stack, and later (while it was still on the stack), it was finalized unexpectedly. I've tried hard to reproduce the problem into a small piece of code, but was unsuccessful.
Before trying the code myself, I thought I'd check that you are running with lua_assert defined? Or at least LUA_USE_APICHECK. Either would immediately rule out the possibility that a bad call is corrupting the stack.
- Alex