What version of xenapp? if you are on 5+ then i would upgrade all clients to receiver and uninstall 9 and 11 first, if your software supports it.
I have seen an old unused xenapp server in the farm slow logins tremendously, at one site we can an old 4.5 server still in the server farm although it was not used. After i removed it from the farm cwi loading times and login times increased fro 40 seconds to 15 seconds.
But it is not uncommon for citrix to come up with annoying errors like, unable to load application. Forcing you to click the application a few times.