I switched to wayland about six months ago too. 
I just tested the exact same workflow on an X11 session and on a Wayland 
session.
X11 sessions do NOT have this problem. On Wayland, this is reproducible 100% of 
the time. 

Also tried the following: invoking geany from an xterm with different GDK 
backends:

xterm with Wayland as GDK Backend 
 - same problem reproduced, same behavior as observed when opening files from 
nautilus, the existing instance is used to open the second file in a new tab 
but geany is not brough up to front

xterm with XWayland as GDK Backend 
 - no issue: opening the second file causes geany to be brought to front, with 
the new file in a new tab








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