HI Aseem, I had the exact same problem but in the opposite order. I bought the Sidewinder 3D Pro installed the profiler software
but never could get the bottom buttons on the base to work. Then when I bought my Sidewinder game pad it came with a new driver setup that updated the profiler both the Sidewinder 3Dpro and Sidewinder Game Pad to a newer version and that is when all the buttons including the base ones started to work.
Here is what most likely happened. Windows98 detected and installed a compatible driver to make the stick work, you installed the profiler for the 3d pro which has older drivers and thus doesn't recognize those base buttons. To fix this issue go to the following url listed below on the Microsoft site to download the 3.02 Profiler drivers and this hopefully will fix your problem.
I have just bought a Sidewinder 3D Pro. Today. I have Windows 98.
When i installed the new Joystick from the control panel, game controllers,
Sidewinder 3D Pro was listed there, I selected it and the joystick worked
fine...i also checked through the calibration and tests all the eight
buttons were working,along with the 8 hat POV's.
Later on i installed the software which had accompanied the joystick, (this
is when the problem started) Now when i test the joystick, only four POV's
work and only four buttons work. The bottom Four Buttons Don't work.. How do
i rectify this problem..
I also tries to uninstall the joystick driver, and when i tried to reinstall
it from the original Win98 CD it was not there.
Please Help me...
Thank's in advance.