Confirmed. This effect is very frustrating, the answer to the problem is counterintuitive but very simple once we understand how ArchiCAD approaches it.
The core of the problem is the follwing -- when a stair is hotlinked to a host file with different story height settings, a couple of things may happen:
1) what you think is the "relevant bottom story" becomes "below relevant stories" or "above relevant story" and receives those display settings.
2) what you think is the "relevant middle story" becomes the "bottom" or "top"
3) what you think is the "top" actually becomes "middle", and so forth.
So, the apparently random behavior is rooted in your original stair display settings.
The solution is that you must define desired display settings for all scenarios, even the ones you don't see in the hotlink file/module.
In the example below, in the hotlinked file, I forced "Show on: All Stories" and then
made a very tall stair that spans across 3 stories
, and only then ArchiCAD showed me all available settings: below bottom, bottom, middle, top and above top.
Hotlink file screenshot above.
All settings are initially visible...
After you do that "programming", change your stair to "Show on: All relevant stories" (or a different display limit) and change the stair to your desired size. Your settings will be remembered and used in the host file:
Host file screenshot above, same stair.
Note the shuffled settings, the "middle" becomes the "bottom".
The "middle" settings from hotlink are applied to the "bottom" in the host.
The explanation above is maybe incomplete, but I hope it makes some sense.
ADMIN: can you please move it to Documentation? This is not GDL related.