### Godot version

Master (0ddd9c3e8f9088fa139e25b2903289d727073e12)

### System information

PopOS 22.04 - Intel integrated graphics - all backends

### Issue description

When there are popup windows in the editor, I cannot click on the "Confirm"/"Cancel" type buttons at the button. 

I have the issue both in the project manager (importing projects I can click on files etc. but cannot click "open") and when running the editor (cannot click "Save&Quit" etc.)

Sometimes the editor correctly highlights the buttons and I can use the arrow keys to navigate the buttons and "enter" to confirm my selection.

_I can navigate the editor closing dialogue with tab/arrow keys_
![Screenshot from 2023-01-16 14-24-06](https://user-images.githubusercontent.com/16521339/212774269-d784ea5e-5921-4460-9124-48978939c8e7.png)

_I can't navigate the project import dialogue with tab/arrow keys_
![Screenshot from 2023-01-16 14-29-00](https://user-images.githubusercontent.com/16521339/212774683-0a80795a-eed4-4e65-b2ca-3562c25d71fd.png)


### Steps to reproduce

Run the editor

### Minimal reproduction project

Reproducible in the project manager
xdnd_aware = XInternAtom(x11_display, "XdndAware", False);
	xdnd_enter = XInternAtom(x11_display, "XdndEnter", False);
	xdnd_position = XInternAtom(x11_display, "XdndPosition", False);
	xdnd_status = XInternAtom(x11_display, "XdndStatus", False);
	xdnd_action_copy = XInternAtom(x11_display, "XdndActionCopy", False);
	xdnd_drop = XInternAtom(x11_display, "XdndDrop", False);
	xdnd_finished = XInternAtom(x11_display, "XdndFinished", False);
	xdnd_selection = XInternAtom(x11_display, "XdndSelection", False);
#ifdef SPEECHD_ENABLED
	
	tts = memnew(TTS_Linux);
#endif
	
	
	rendering_driver = p_rendering_driver;
	bool driver_found = false;
#if defined(VULKAN_ENABLED)
	if (rendering_driver == "vulkan") {
		context_vulkan = memnew(VulkanContextX11);
		if (context_vulkan->initialize() != OK) {
			memdelete(context_vulkan);
			context_vulkan = nullptr;
			r_error = ERR_CANT_CREATE;
			ERR_FAIL_MSG("Could not initialize Vulkan");
		}
		driver_found = true;
	}
#endif
	
#if defined(GLES3_ENABLED)