Build 1.6.1 is now available to download, but seems to use a much more different structure this time since we actually have to manually download it. Also, please bare in mind the server updates are not instantaneous to when each update is released. Plugins also need to have updates first before doing so, otherwise, things will break, and bad things can happen. Also, updating too soon will cause you to be"locked out" of the server till up to date so remember that as well.
Extra Note: Oh, and word of warning, if you're one of those who has like over 10 plugins/mods in their Minecraft.jar and such, be ready for a headache to update and patch them for usual reasons.