If the issue you stated persists even after a clean installation, the next step would be to remove all internal or external devices that use non-Apple device drivers from your computer system. These items might include: internal or external hard drives formatted with 3rd party utilities, NuBus cards (for example, accelerator or video cards), or any other non-Apple hardware.
The reason that you should physically remove these items is that all device drivers are ALWAYS loaded at system startup regardless of the designated startup disk. In other words, booting from a Startup Diskette or CD (like Disk Tools) does not eliminate all third party software from the startup sequence if there are still non-Apple items in or attached to the computer. Those devices will continue to load their driver software at startup from any startup disk.
If the issue continues even with all third party devices removed, the next thing to try would be to remove any extra RAM that has been added to your Macintosh. If removing all extra RAM still doesn't resolve the issue, you may have a computer hardware issue that needs service.
For information about how to perform a "clean installation" procedure search with the string, "clean installation".