Internet Explorer Enterprise Mode

We have recently made the jump to IE11 (from IE9) and are using Enterprise Mode to render previously incompatible websites in an IE8 emulation mode.  We have 25 sites in our 'sites.xml' config file and have applied the necessary registry keys to (a) enable EM and (b) direct the browser to the sites list.  This all works perfectly well except when browsing our CRM site (we use web-based Lexus Nexus InterAction).

Generally, the home page will always render correctly but when attempting to 'add an activity' to a contact, the popup window which appears seems to throw the browser out of Enterprise Mode.  The result is the text boxes and layout distorts and eventually the browser locks up and has to be killed in Task Manager.

Thereafter, when IE is next opened the Enterprise Mode fails to start.  It can be switched on manually from the Tools menu but this only temporarily activates it for the current page, it doesn't seem to force the browser to re-evaluate the sites list and start working properly again.  Selecting Tools | Options | Advanced | Reset in the browser then closing and re-opening it, will re-invoke Enterprise Mode.  It will continue working correctly until the InterAction site is browsed again.

Has anyone experienced issues like this with Enterprise Mode, in particular in a legal environment using InterAction?

We are using Windows 7 x64 clients in a Citrix XenDesktop (non-persistent) environment with AppSense to apply application settings and retain user personalisation, in lieu of roaming profiles.  I have applied the necessary AppSense exclusions for Internet Explorer (prior to this, EM was not working at all).
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mills-reeveAsked:
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mills-reeveAuthor Commented:
This has been resolved by enabling Enterprise Mode in HKCU not HKLM.  MS documentation suggests HKCU for the current user or HKLM for all users.  We are using XenDesktop non-persistent PCs with AppSense so I used the HKLM registry key in a process start event for Internet Explorer.  I think this may be why it kept dropping out intermittently.  Since applying the key in HKCU instead, it has remained stable.
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