Hi,
There were lots of filetype patches recently, but any changes in the global filetype commands (via Build -> Set Build Commands) are still buffered and saved on Geany quit. This is out of sync with the other settings, inconvinient, and makes the code a bit more complex. Here is a patch that saves the filetype command changes as soon as OK is chosen in the dialog. It's not any different from the same patch published several months ago, only updated to the latest svn.
Note that the non-filetype ("independent") commands are still saved together with the other geany.conf settings, on Geany -> Quit or Edit -> Preferences. This can be altered by moving build_save_menu() from save_dialog_prefs() to show_build_commands_dialog(), but I'm not sure we want it, and the global command changes are rare anyway.