Windows ME shut down problem

I am running windows ME as the primary operating system, with w98 as a backup on a second hard drive. ME and 98 cannot run at the same time, as they are switched through the BIOS startup routine. Just lately I have been having the following message:
windows write protection error
you must restart you computer
when I have been shuting down. On restart, the scandisk turns up a boot error, and corrects it.
1. what is causing this problem,
2. how do I sort it, and
3. is it doing any lastingdamage?
Its not causing any other problems that I can see, just beeing annoying, which is why I changed from 98 in the first place.
Your help is appreciated.