I have this problem, as well with MSDE as with SQL server 2000, on different servers :
the serverdisk starts turning like a fool for quite some time and access to the sqlserver isn't possible anymore. After some time (I guess 20 minutes) diskactivity stops (gets to 'normal') and SQL server is accessible again.

What's my problem ?

What is your problem I could say from Bulgaria, but I can explain you when this happaens with our testin SQL Server.
- when my programmer try to send bed done query. I solve the problem optimysing queries myself
- when you make delete, update all you operations first ware write in log file and after that executes. If you make this in a bunch, that operation thatcould be the second reason.