Posting over on the App-V team blog reports that applying ConfigMgr 2007 SP may break App-V file type associations ...

When you upgrade a computer that is running the App-V 4.5 client to System Center Configuration Manager 2007 SP2, it may break all the File Type Associations (FTA's) for the virtualized applications.  This can occur because the SP2 installer updates the following key in the registry as part of the Configuration Manager 2007 Service Pack 2 upgrade:

HKEY_CLASSES_ROOT\SCCM.VAppLauncher\shell\Open\command

But it does not update the other two keys that App-V uses:

HKLM\SOFTWARE\Microsoft\SoftGrid\4.5\Client\UserInterface - DDELaunchMSICommand and LaunchMSICommand

This causes all the FTAs that were created through a published APP-V application to break, until a time when a new application is published to the machine which triggers the client to update the key itself.  At this point the [Read More...]

Read the complete post at http://wmug.co.uk/blogs/r0b/archive/2009/12/18/upgrade-to-configmgr-2007-sp2-may-break-app-v-file-type-associations.aspx