Our web application, is used in a few countries controlled by a central citrix server . However, some users from a few countries seems to get an error 'system call failed' on different screens, sometimes when the server is busy and sometimes when the load is not heavy.

The system call failed comes in two types :

An error has occured in the script on this page:
Line : 1
Char : 1
Do you want to continue running this script on this page?

or Line : XXX
Error : system Call Failed
Please Contact your system Administrator.

Based on the google searches , I have already verify and turn of the script debugger and display notification setting in IE. However, the issue still persists.
Since it happens sometimes on different screens, I`m not sure what or where is failling. There is alot of javascript validation and functions running on the window. All the javascript is on a pop up window (minimized ) (small win) . A user can only open up to 4 windows/ sessions and any javascript validation call has to go through the small window. Once the small window is closed, the whole application will be closed. It seems like, at times, the window loses the reference to the small window. Is this possible?

I would really like to know, what causes 'System call fails'. and what good javascript practises I can do to fix this problem.