Need better WebSphere Application Server Performance for

Joe, Nathan, et al,
 
I think I've confused you all; let me try to make it a little clearer
than mud.
 
The application, I'll call O (I'm hiding the real name so you won't be
adversely influenced), can be installed three ways:
 
1. O for Windows -- In my case installed on one of my partitions blade
servers  -  Performance is excellent so no tuning needed here.  
 
2. O for WebSphere -- Installed on a Windows blade.   So on the blade
is O for WebSphere and, of course, WebSphere Application Server so the
application will run  -  
 
3. O for WebSphere -- Installed in the IFS of one of my i5 partitions. 
 O for WebSphere is installed and WebSphere Application Server so the
application will run.
 
Both O's for WebSphere run like a herd of turtles in a cloud of wet
cement.   I need one of them to run faster.  I'd prefer it to be the
IFS/i5 install.
 
When I do a query of a file that is about 1.4M rows with the O for
Windows, my response for the first 20 rows is about instant.   The same
query with either O for WebSphere is about 4-5 seconds.   Acceptable.
 
When I try to go to the bottom of the table I know it will run into a
parm I've set to limit rows returned but this kind of experiment will
show me how fast the product goes through the table.  The MAX ROWS
ALLOWED parm is set at 10,000 rows.   With O for Windows the application
gets to MAX ROWS in about a second.   With either of the O for WebSphere
installs, the query still has not gotten to the "hard stop" after 3
minutes, at which time I kill the query.   VERY BAD.
 
My assumption is WebSphere is causing some performance problem as
that's about the only difference in the application versions.   How do I
TUNE WebSphere or whatever needs to be tuned to make WebSphere allow my
O for WebSphere applications to run faster?
 
Hope that's clear.
 
Thanks for your patience,
 
Dave Odom