Select multiple files in the project tree, right-click and hit properties, change anything - especially the "compile file" and "link file" toggles on the second tab, or the "use custom command to build this file" setting, and when you "OK" out of the dialogue, the changes are only applied to the first file.
This is a hassle because I often need to specify the same custom build command for large numbers of files, and have to resort to manually editing the project file in those cases.
This happens on the current Linux system, and I seem recall it happening on the last Windows nightly as well.