In my XenApp 6.5 Farm my published applications would not run in Seamless mode. They all had the desktop wrapper around them. My internal web interface site launched the applications seamless as expected by my external website reached by users coming in remotely did not.
All my installs were pretty much out the box. The only slight thing worth noting is that the web interface box was an install via XenDesktop installation. I then use this web interface site to allow connection to both my XenDesktop and XenApp environments. I have a site set up for LAN users and another setup for External connections.
To resolve the issue i had to add TWIMODE=ON into the default.ica file in the external website directory.
This file lives in Inetpub\wwwroot\Citrix\xxxx\conf where xxxx is your website path
I got this information from this article
http://support.citrix.com/article/CTX116357
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