Scenario: 2 Citrix XenApp farms (6.5 and a 4.5)

The 6.5 apps were always appearing and working ok

The 4.5 apps would sporadically appear or even disappear during a refresh of the Gaeway page ‘ Some applications have been removed’ even if these applications had the option to allow via access gateway UNTICKED

Solution:

One of the 2 servers for the 4.5 farm did not have the Trust XML option enabled, once this was enabled the application stayed hidden!