Hmm, that is very strange. If it is showing the lock icon there then it should almost certainly be locking the apps. When you click Apply Changes does your phone lock? Otherwise if you could go and run applock -d from a normal terminal (not as root) and tell me what it says?

You could also try removing your settings.db file (in /home/user/.applock) after uninstalling it, and then reinstalling it. Uninstalling it doesn't remove the settings.db file.

I have pushed v0.3.2 to the autobuilder and my website, same links, which fixes the problem with the menu and the problem with adding binary applications (forgot to add the new settings management code to that function).

EDIT: Also pushed the latest source to Git if anyone wants it.
gitorious.org/applock-n900

EDIT2: Okay, well it looks like the menu bug was fixed and replaced with another variant of exactly the same bug :P. Will fix that in v0.3.3. In v0.3.2 it has a white background rather than a transparent one, meaning you can't see menu items behind it. Not a massive problem but it will aggrivate me until I fix it