This can happen for a number of reasons but all of which relate to how long it takes for the users profile to load. Old printers in the profile, lots of temporary files, a big profile and GPO WMI filters can all be culprits causing this. The default timeout is 60 seconds. Citrix article, CTX126673, goes over the WMI filter issue and the resolution is to remove these filters, not really helpful if the problem in your environment is not related to WMI filters. There are many forum entries regarding this but none provided the actual fix.

Hotfix Rollup Pack 3 (CTX138537) for XenApp 6.5 contains a previously released hotfix (CTX132912) which lets you modify the default timeout value. After this hotfix is installed you can modify the registry as below on each server where the application is published.

A session can be terminated before the first application launches. The issue can occur when a one-minute time-out is exceeded, for example, when the profile share is located across a WAN link rather than on a local share. This fix introduces support for the following registry key that allows you to configure the time-out as below.

Name: ApplicationLaunchWaitTimeoutMS
Data: <desired additional time-out, in milliseconds>

Note: Specifying a value of less than 10000 reverts to 10000 because 10 seconds is the minimum override.