After activating the Auto-mark plugin, Find → Find All → Mark no longer marks all matches. Deactivating the plugin restores normal behaviour.
My system is a Debian 9.5 (Stretch Stable) with XFCE. Both Geany and the Auto-mark plugin have been installed from the Debian stable repository. The output of `geany -V is`: `geany 1.29 (built on 2016-11-16 with GTK 2.24.31, GLib 2.50.2)`