Java application slow in Citrix since IE9 upgrade

Can you try to disable your antivirus tool on your xenapp server an check, sometime security tools may cause the issue.

You could experiment with Progressive Display, if you're not already using it: http://blogs.citrix.com/2011/05/30/hdx-progressive-display-dont-forget-to-turn-it-on/

This issue is complex and relates to flash player rendering. Although I am not running this particular version of Citrix the behaviour seems the same in that issues occurred since IE9
http://discussions.citrix.com/topic/293396-there-is-no-way-i-can-get-flashredirect-to-work/

HDX MediaStream for Flash is a technology whereby the flash objects are transferred from the server to the client and played locally. There is no equivalent for Java.
If you don't use HDX mediastream for flash then you have to render the flash on the server desktop and transfer it as bitmap images to the client each time it changes, which is usually rubbish. This is what is effectively happening with Java too. Progressive display can help to an extent, but the ICA protocol isn't designed to do this kind of transfer and I ultimately dumped XenApp as a result (HDX MediaStream for Flash is not perfect, some popular sites don't work properly with it).

Thanks, really good informative replies.