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> If I don't do anything (don't pop values, don't use checkstack and don't
> use lua_settop(L, 0)) I run out of memory, no surprise there.

There is no need to lua_settop(L, 0) if you're in a C function called by Lua.
There is, however, a need to call lua_checkstack/luaL_checkstack if you
use more than 20 stack entries.
> How is proper stack handling supposed to be done?

Perhaps rebuilding Lua with LUA_USE_APICHECK on will help pinpoint the problem.