We have the problem, that google chrome, installed on a Windows 2008 R2 SP1 Enterprise Server with Citrix XenApp 6.5 is not recognized as installed application, and because of that even not patched, on normal Windows 7 machines google chrome is normally detected.
Working as designed as Chrome doesn't support th Windows Server platform:
https://support.google.com/chrome/answer/95411?hl=en
Alternative solutions:
1) Use Firefox instead of Chrome as Mozilla supports Windows Server:
https://www.mozilla.org/en-US/firefox/29.0/system-requirements/
2) Create a software package containing the installer of the new version of Chrome and distribute it towards your Windows Server machines.
3) Clone the Chrome definition you want the server machines to be scanned against, creating this way a custom definition. Modify the custom definition to include, in the affected platforms, the Windows Server versions you want to deploy the update to.
Since the Chrome updates are cumulative, there is no need to deploy every single update, but deploying the update including the latest version should be enough to have all the systems updated to the current release.