Hi,
Kayes,
As usual,
Zeldrak is spot on with the correct answer.
Heirlooms quit scaling after a certain point. There are certain 'inflection points' while leveling where even greens will beat Heirloom gear. The algorithms the bot uses to evaluate gear should apply to scaled Heirlooms as well as normal drops.
In short, the bot should be making the correct gearing decisions at all times, including Heirlooms. (Trinkets being the exception.) If not, please make a new thread in the Support forum with a full log of the 'bad choice'. If there's a problem with the gear evaluation mechanisms, its something that should be corrected.
cheers,
chinajade