Every once in a while Geany has an issue where it's set to always on top. I've had this issue intermittently for years (since before v2) and I've never been able to figure it out.
When this happens Geany does not show up with wmctrl, taskbars or anything else that lists windows aside from xprop. When Geany is stuck in this state xprop always reports the window has _NET_WM_STATE_ABOVE set but nothing will remove it. The only fix I've found is to close Geany and reopen, test if it will go below then rinse and repeat as it normally takes 5+ tries before the above state is cleared or lost.
I'll also note there is only one instance of Geany that does this which makes me think somehow a setting in the one instance is intermittently causing the issue.
I've encountered this under XFCE and CTWM.
Geany 2.0 (built on or after 2023-10-23) Using GTK+ v3.24.43 and GLib v2.82.2 runtime libraries
This sound more like a function of the DE/WM. Is it possible that you accidentally pressed a keyboard shortcut for always on top? Quick google search suggests that in XFCE this can be done by pressing Alt+F12 or Alt+Space followed by T.
That would be a solid no. There is no Always on top hotkey in my WM (XFCE was a long long time ago before GTK broke XScreen enumeration). That said if I had hit some always on top toggle, pressing it again would remove it and as I've said, nothing will remove it. I've tried every tool I could find that can manipulate windows and when this happens as the OP says -NOTHING- will remove the _NET_WM_STATE_ABOVE state.
How often does this happen? Do you use any plugins which could modify the window state?
I use Geany since it exists with Xfce and never experienced this.
You said you use multiple instances, do they share the same config or has each instance its own config? If the former, does it happen on the first Geany window or any of the later created windows?
Do you use something like "devilspie" or so which could interfere?
It happens maybe once a month. Plugins = Addons Auto-Mark Pair-Tag-Highlighter Spell-Check Tree-Browser (so no...in theory)
All instances have their own configs. If I say rename the offending config to config.old and restart it will be fine. If I then rename the config to be used the problem returns, until you restart geany over and over.
Devils pie is ancient heh no I don't use it.
There seem to be only two places in GTK where `_NET_WM_STATE_ABOVE` is set: - by using `GDK_WINDOW_STATE_ABOVE` - or by calling `gdk_window_set_keep_above()`
None of the two seems to be used by Geany or geany-plugins so not clear where it comes from.
And there is nothing GTK based that touches window states on my machine. Xprop, wmctrl or CTWM is are the only things.
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