On Linux (at least under Gnome 3), If the "build options" dialogue is open for a project, it holds the foreground. However, if the project file is externally modified during that time, the "reload the project?" dialogue pops up behind the build options dialogue, but captures input. There's then nothing you can click in the "build options" dialogue to close it, and you can't reach the "reload?" dialogue because it's behind the build options.
Can you reproduce this behaviour in another window manager like fluxbox? I don't have gnome3 nor have the desire to install it? It will force me to switch to systemd, which I don't want to do.
Also what distro exactly are you using? What gtk and wxgtk versions, too?
Distro is Debian Testing, and all versions are the up to date defaults for that. Gnome-shell 3.22. Libgtk is 3.22.0-1. There are two libwxgtk packages installed, 2.8.12.1-12 and 3.0.2+dfsg-2.
I'll also test on other WMs when I get the chance.