As the others have stated, you're using a system that is marginal for the application. But I think it can be made to run smoothly, you'll just need to tweak it for the maximum possible performance.
Go to this site,
http://www.blackviper.com/ , and turn off all unecessary XP processes. I'm assuming that you are running XP.
Make sure that all video and memory settings are set to the fastest possible speeds in the BIOS.
Overclocking the system a little couldn't hurt.
The motherboards L2 cache (which is now L3 cache with a K6-3) may be hurting more than it is helping. I've found that it limited the FSB on some socket 7 systems I've overclocked. Try disabling it in the BIOS. If it doesn't seem to make a difference though, I'd leave it running.
As Jupiter mentioned, a different, possibly less resource intensive, DVD program may help.
What motherboard are you using? Does it have proper BIOS support for the K6-3? If you can find a newer BIOS than what you have, it wouldn't hurt to update. If AMD features like Write Allocate aren't supported, it will limit the CPU's performance