Performance Issue

Hi,
One of our applications is experiecing slowness (about 2 mins for a simple report) while running reports. These reports when tested within Query Analyzer execute faster ( 0 - 1 sec) with using appropriate indexes as per the execution plan. Also with data being loaded with this new app, we have probably 10 users logged in.
Setup is as follows:
64-bit Windows EE 2003 R2 SP2, 64-bit EE SQL Server 2005 SP2 iSCSI Cluster, Network Load balanced 64-bit SE Windows 2003 R2 SP2 App Server.
I directed the application server to point to other SQL cluster with same configuration , and the reports worked faster as expected. Logged into the application server, ran this query from Query Analyzer, worked faster as expected.
I'm still lookign into the cause but would appreciate any help..
Thanks