We are using the latest version of Pulse Desktop Client 9.1 and it is having the same issue. every time, we are asking end-user to go to Task Manager and maximize the authentication window to provide input.
@yesuveeranki Can you please involve Microsoft to look into this issue and see if they have any RCA/fix for this issue? Taking a procmon log should capture some info about the way how the application starts and how it behaves.
Better solution is to fix registry keys for window position. To do this please: