I have a dual-boot system with WinXP Pro and Win98. The ships definetly move faster under Win98 than under WinXP. It's a dual-boot system, so it's all the same hardware.
It's annoying more than anything, although I furrow my brow mightly when I play under Win98 and see the ships zipping across the screen...
I run se4 on two systems under XP. one is a high-spec 2.something desktop (work) and the other is a 1.4 Sony Vaio laptop (my own, my precioussss). On the laptop I've played se4 both before and after installing the 4 in 1 drivers.
Never noticed any irritating slownesses on either machine at any time.
You can try to use Win 98 compatibility mode. This is how to do it:
Make an icon of SE4 - right click on it - select properties - select compatibility - check "Run this program in compatibility mode for" box - select Win 98/Win ME - click apply.