You might be aware that a new version of Flash Builder 4.6 was recently released. Along with that release, Adobe also released Flex SDK 4.6. Unfortunately, Flash Catalyst projects are not compatible with the new SDK.
The reason for this error is that Flash Builder 4.6 does not come with Flex SDK 4.5 installed. You can manually install this SDK, and you should not have any issues.
If you would like to convert your project to use Flex SDK 4.6, there are a few steps you need to perform. The first is to disable the Automatic Check Compatibility function. Note: You can not do this in the Project Properties panel, it must be done via the menu.
With the Flash Catalyst Checking disabled, bring up the Project Properties panel.
Change the SDK version to 4.6 from 4.5. Click OK. Your project will now compile under the new SDK. However, this means you will no longer be able to round-trip the project with Flash Catalyst.
Hope this quick post helps.