Well I know what your problem is now. Glide was the propriority API (intead of OpenGL or Direct3D) which was only for 3dfx cards. If you are running any game and are trying to uses Glide, you need to change the settings to OpenGL or Direct3D. Also did you do a clean install of Windows. If not it is likely you did not completely uninstall the drivers for the Voodoo cards and this could be the source of your troubles. Refer to the article on www.guru3d.com about making the switch from Voodoo to GeForce for further instruction.
You don't have to reinstall Win 98. Get a Glide Wrapper. It is a program/files that interprets Glide code to be read like DirectX or OpenGL so any graphics card can support it. Then you can change the display type inside D2. Go on a search engine and search for some.
If you have an actual Windows 98 SE disk and a Windows 98 SE startup disk then here's how to uninstall Windows. I'm assuming you only have one HD and didn't partition the drive. Boot up from the floppy. When you get the A:\ prompte type in "FORMAT C:\" This will reformat the hard drive and erase Windows. Once it's done formatting boot from the Windows 98 SE CD and begin installation.