geany will sometimes ignore an existing socket/instance and will open a file in a new instance.
One way to consistently trigger this:
# Open a root instance
gksu geany atextfile &
# Open a normal user instance
geany anothertextfile &
# Now manually CLOSE the root instance window
# Now open another file as normal user
geany yetanothertextfile &
yetanothertextfile will be opened as a new instance instead of reusing the existing socket.
Part of this behavior may be related to this bug...
Arch Linux x64 geany 0.18.1-1 running under Openbox