It really sounds more like a bandwidth issue or a resource issue at site A. Have you done any monitoring when the issue occurs? Have you asked your user with an issue to run a continuious ping to the citrix server, and take a look when he/she is experiencing an issue. Is the latency abnormally high?
Also, take a look at the Citrix server to see if someone is running an app that is taking up alot of power on the server, this could be the issue.
In terms of roaming profiles, You should take a look at the profiles and note how large they are getting. Hugh profiles can get problemattic especially when users are roaming to servers that they have not yet connected to for the first time
a quick question on the user configuration
is there user drive mapping or printer mapping to local
is sound turned on
and the classic is there an open gl screen saver on the server(unlikely but have to ask)
What colour depth are you running the RDP session in?
RDP commonly runs at 256 colours and ICA runs more often in 32bit full colour. This can explain the difference in performance. To test - try running the application in 256 colour through ICA.
Also check the encryption level of the ICA traffic - shouldn't create much of a slow down but can be an overhead to take into account.
The main difference between RDP and ICA is that ICA has been optimised to run faster over lower bandwidth connections with Speedscreen type technologies. If you're mapping printers and client devices in both RDP and ICA then that's not likely to be your problem.
VMWare can quite often create performance problems for Citrix. Brian Madden has written a few articles on the matter -
www.brianmadden.com. Can't lay my hands on any at the moment. Specifically he talks about paging being a major issue with VMWare and Citrix as the disk subsystems can rarely keep pace with with the paging required.
In the meantime if your create a baseline for the Citrix Server in perfmon whilst the user is not using the problem app. Then create another when they are hopefully you'll be able to see what resources the application is utilising and then be able to identify what's causing it. In the baseline i'd include CPU utilisation, number of sessions, memory usage and disk queues to start with. if you want you can look at the "process - private bytes" and "process - working set" plus pages in and pages out. Though to be honest unless you're looking at memory optimisation tools then this can be a bit confusing.
