Since no comment has been made by Automatic or the developer, I figured I'd make an update here. The plugin will still work with WordPress 3.5.1, but only if you adjust your custom HTML code.
If you have any quotation marks in your code (within the settings panel of plugin), strip them out. Otherwise, the new WordPress environment, for whatever reason, will insert extraneous code (slashes) wherever these marks are found.
For instance, if you have code that looks like this:
<font size="1" color="#999">
Change it to this:
<font size=1 color=#999>
Your signature should now look normal again.