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>Which platforms are development and target? Both PC (because of your
previous titles)?

Both PC - good guess!

>Do you have a different memory manager in the game? (i.e. lmem.c has
been touched). Could be a bug in allocation or realloc (when table size expands past 64).

We do have a different memory manager but we've been using if for a couple years now and haven't had any problems with it, I will look into this a bit closer though.

>Have you been into llimits.h and made sure that Lua is tuned the same between both platforms? i.e. both float or double. long has a different size on some platforms, e.g. PS2 is 64 bit long and PC is 32 bit. Lua does some header checks on compiled code though. It should catch most of these issues including endianess, which it deals with (or does in 5.0 anyway).

No changes to llimits.h.
But would any of this explain the difference when dofile runs a text file and a precompiled binary file? 
Thanks for the quick response.