Symptoms
From some Windows XP machines using online plug-in 11.2, you cannot use the mouse properly in a Seamless Application on XenApp 6.
The mouse pointer will be about two inches to the right when you click.
The issue does not occur in a fixed Window.
If you use the Shift+F2 key combination to change from Seamless to a Fixed Window, the application screen starts flickering and does not stop until you close the application.
Resolution
Upgrade to Online Plug-in 12.1 to solve the issue.
This document applies to:
Source: CTX127897 – Cannot Use the Mouse on Seamless Applications on XenApp 6 – Citrix Knowledge Center