I was getting ready to release a map today, but as soon as I tested the map after using the final compile I noticed something was wrong.
Almost all of the grate texture enclosing a space behave strangely with light. It is as if the light does not pass through them. The surfaces inside appear either completely black, or covered with dark yellow-green splotches that mean they aren't being lit.
Again, this did not happen until I used the both-final compile option, so I'm assuming it is somehow related. Thanks in advance for any help or ideas as to what caused this.

I assume you have cubemaps entities in your map and you build cubemaps after the compile?

if you want your grates to not cast shadows behind them, convert them to func_brushes and disable shadows.

There are a few less known options for vrad that affect shadows cast by props.
Have a look at this thread.

Thanks you two, I had no idea grates cast shadows like that. Just to be clear, those commands appear to do what the final compile usually does, but more efficiently?