"To our knowledge, all outstanding issues being cause by Lion are for FCP only. Magic Bullet products in other host applications (like After Effects) work fine."
From Red Giant's Head of Engineering:
The release of OSX 10.7 (Lion) introduced a bug into FCP7 that we have been unable to find a way to work around. We have contacted Apple and are waiting to hear when they will have a fix (either in the Operating System or with Final Cut Pro). This bug affects any plugins for FCP that make use of custom data. Essentially, Apple provides two methods for storing data related to a plugin – general sliders, for example, are a built-in method that Final Cut Pro provides for storing data related to an effect with your project. For more complex information, however, a plugin can define its own set of custom data that it will save within the project. This second method of storing data about an effect with your project is currently broken in the FCP7 / OSX 10.7 combination. It works fine when you run FCP7 on OSX 10.6 (Snow Leopard).
Unfortunately for Red Giant plug-in users, we make use of custom data in both the Looks 2.0 and Colorista II plugins. The end result of this is that, while you can use the plugins with FCP on Lion, part of the data associated with the effects once they are applied will not be saved.