We want to distribute a number of applications (including several App-V 5.0 plugins) and packages by using a task sequence. The execution of the task sequence works fine, however our to App-V virtual groups are not registrated as App Connection Groups in the Microsoft Application Virtualization client. The virtual apps are therefore not working properly, and making the task sequence unusable.

We have distributed the same number of applications, plugins and packages by using software distribution to separate collections and it works without any problems.

First, are you using the Application Model for deploying the App-V 5.0 applications? Application Connection Group comes in place when the Application Deployment Evaluation Cycle is run. That shouldn't have anything to do with the deployment with TS, or atleast I think so. Have you tried running the App evaluation cycle manually after the TS has run?

"Virtual environments are created or modified on client computers when the application is installed or when clients next evaluate their installed applications. You can order these applications so that when multiple applications try to modify a file system or registry value, the application with the highest order takes priority."

http://technet.microsoft.com/en-us/library/jj591609.aspx

Have you configured the Connection Group in the console?