You will have to modify the GDL Script of the Label used for this.
You can set Windows for their Sills to be measured relative to the Floor Level of the current Floor. To get the height value you need you will need to add to this the vertical distance between the floor level and the Project Origin. There are GDL Global variables for this purpose, you will probalby need the GLOB_HSTORY_ELEV variable.
http://www.archicadwiki.com/Global%20GDL%20Parameters#StoryInformation
Be aware that this article is old so some things might work a bit differently with AC12.
Get Archicad Tips at https://twitter.com/laszlonagy
AMD Ryzen 1700X CPU, 48 GB RAM, Nvidia GTX 1060 6GB, 500 GB NVMe SSD
2x28" (2560x1440), WIN10 PRO ENG, AC20-AC26
Loving Archicad since 1995