There are 3 potential work arounds for this issue:
1. The ConfigMgr client agent takes managing virtualized applications when “Allow virtual application package advertisement" in the Advertised Programs Client Agent properties in the ConfigMgr console is checked. If this box is unchecked, it is then possible to run both ConfigMgr and App-V client agents at the same time. To modify this setting, open the ConfigMgr Console, expand Site Database, Site Management, <Site Name>, Site Settings, Client Agents; then open the properties for Advertised Programs Client Agent. The next time the client agents refresh (or if you kick off a Machine Policy Retrieval & Evaluation Cycle), the App-V client will become the default handler again.
2. The second option is to manually modify the registry keys on the client back to the original values. Thus, we can make the following modifications:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\SoftGrid\4.5\Client\UserInterfaceChange to the following:
LaunchCommand "C:\Program Files\Microsoft Application Virtualization Client\sfttray.exe" /launch "<APP>"
DDELaunchCommand"C:\Program Files\Microsoft Application Virtualization Client\sftdde.exe" "<APP>" <DDE>"However, keep in mind that if “Allow virtual application package advertisement" in the Advertised Programs Client Agent properties in the ConfigMgr console remains checked, it is possible that it will reset the registries to their previous values and the issue will reoccur.
3. The third option is to use ConfigMgr to manage the virtual applications instead of using the App-V management server. More info on this can be found here:
http://download.microsoft.com/download/f/7/8/f784a197-73be-48ff-83da-4102c05a6d44/APP-V/App-V_and_ConfigMgr_Whitepaper_Final.docx