With an update as large as ComputerCraft 1.6, it was inevitable that a few bugs would slip through testing. This update addresses those. Specifically: it fixes cases of Computers not rebooting on Server restart, and of new Computers with different IDs all sharing the same folder structure. Enjoy!
ComputerCraft 1.61 requires Minecraft version 1.6.4 with an up to date version of Minecraft Forge installed. Once you have Forge, drop the files into your /mods/ directory, and launch Minecraft.