loosing registry

I am running windows 98se and from timew to time it says it encounters a problem with the registry and will restore a recent backup. After it reboots it restores a backup from when windows was first installed and I cannot run any of my programs. I have to reinstall them to make them work and some won’t reinstall at all. I sarted making a backup of the registry and saving it to my desktop so this wouldn’t happen again but when I reinstalled the saved backup it didn’t help. Any ideas?