For some reason, the following if statement is always evaluating to false, even when a factory has been completed.

    if (AITechCount(player, c_TB_Factory, c_techCountCompleteOnly) > 0 && AITechCount(player, c_TB_FactoryTechLab, c_techCountInProgressOrBetter) < 1)
    {
        TriggerDebugOutput(1, StringToText("Blah"), true);
        AISetStock(player, 1, c_TB_FactoryTechLab);
    }
Even though it's a direct copy from the Barracks techlab code (obviously with barracks replaced with factory) which works just fine.

I was just about to post that apparently c_TB_FactoryTechLab in AITechCount counts ALL tech labs, regardless of what they're attached to. Which is very, very annoying. Even removing the second condition won't build one if there's already a tech lab using AISetStock(player, 1, c_TB_FactoryTechLab);

So I've discovered a few things...

TechTreeUnitCount(player, unit or building, const) will return the correct number of tech labs or reactors, so if used in conjunction with AISetStock, you can have it build the correct amount automatically as demonstrated below.

AISetStock(player, 1 + TechTreeUnitCount(player, c_TB_BarracksReactor, c_techCountInProgressOrBetter), c_TB_FactoryReactor);
This will build 1 Factory Reactor regardless of how many Barracks Reactors you have.