What compiler did you use? I would guess Visual Studio 20xx, or are the cross-compile tools for MinGW on Linux workable for 64-bit Windows now?
I know you are putting this as a 32-bit vs. 64 bit difference. But I suspect something else could in play here.
You would think that the way two IEEE 754 floating point 32 numbers are multiplied in asm would be the same regardless of source code. If you see what I am suggesting. The instructions produced must be different.
Also: Isn't what the 32-bit WinQuake does the gold standard? The 32-bit WinQuake is Quake. What I am implying is that in your previous 32 bit vs. 64 bit, the 64-bit version was acting wrong. What I am suggesting is that the behavior of the 32-bit WinQuake can't be wrong and superceding that is a change. The changed behavior could affect tons of little hard to find things in a great many maps, putting things that weren't in shadows into shadows or putting things in shadows outside of them and changing lighting subtly away from what the author was testing against at the time of creation, etc.