Set your AGP transfer mode to the highest possible. Should be either 4x or 8x.
Install the most recent driver, should be Catalyst 10.2.
Maybe the GF 4 is using a DX7/8 render path whereas the RAdeon is using a DX9 renderer.
I've got around 7000 points in 3DMark 01 with a Radeon 9600 Pro and a Pentium 3 @ 1035 MHz under Win 98 SE with the Catalyst 6.3 driver.