I wrote about the issue of Internet Explorer and AppV here before. Long story short, Citrix changes the iexplorer.exe launch handle to point to its own stub of iexplore.exe. I suggested changing the iexplore in the registry to point to the proper version of IE, but the Citrix version appears to be a FTA (File Type Association) stub of some sort. Another solution would be to use the full path to iexplorer.exe (C:\Program Files (x86)\Internet Explorer\iexplore.exe) in the path of the published Citrix application. This avoids the stub being launched.