XenApp and XenDesktop support 2 versions of Flash. The native version (v1) and the new version (v2). The newer versions of XenApp and XenDesktop support both but in combination with some type of Citrix ICA client/Receiver versions it can revert back to the older version.
This is an overview of the used version of Flash support each product uses with a certain client.
|Receiver for Windows||12.x||V1||V1||V1||V1|
|Receiver for Linux||12.x||N/A||V2||N/A||V2|
|Receiver for Mac||11.x||N/A|
You can read the original KB article here.