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By default, Windows 2003 Terminal Server will have a feature called Data Execution Protection enabled. This will cause AQT to crash on startup, unless DEP is switched off for AQT.
This subject is discussed in more detail in Data Execution Protection.
Once this has been resolved, AQT runs fine under Windows 2003 Terminal Server.
The notes in the section Installing AQT under Citrix are also relevant to this environment.