There's a lot of cheap mobos with VIAs chipsets, and some have problems or extrange incopatibilities, other boards could be even broken in parts. I always site for example the Epox 8KTA or 7KXA, the green line issue, an incompatibility with MS-Backup in Win98SE that other mobos using the same chipsets don't present. The surce of this problems varies, but lack of testing would be my choice. Recently I sow a SOYO DRAGON that refuse to power a USB ZIP 250 external.
Other reasons are the problems with drivers, since neither Win95 nor 98 fully understand these chipsets, and a proper OS installation is for meny people confuse. Also, some few cards didn't contemplate AGP diference betwen Pentiums and Athlons, for example the Creative Anihilator II, rewrites your AGP driver with a Pentium generic, therefore you run the APG at 2x, and experience hangs.
The solution is buying a top brand mobo and using it with a modern OS. I strongelly recomend ASUS, any one, even the ALI chipsets ones.