Thin clients or desktops? I know of a few thin clients that support dual monitors. If desktop, have you checked the display applet in the control panel to see which monitor is set as primary?
If you go to the Management Console, and then properties for the application, then to Application Appearance, are you using a custom session window size?
We were having the same problem on one of our clients. I uninstalled the ICA client and started from scratch. That worked.
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