The READ_COMMITTED_SNAPSHOT option can only be set if you are the only connection to the database. So when you see that command running for a long time, it is waiting...
We've seen this happen on a few customer databases over the past couple years, mostly when running on Windows 2000. All the problems I have seen were fixed by service...
Here's a great article on MSDN about using MSDE 2000 in a web application. It describes how to get around the connection limit by setting the Max Pool Size for ADO.NET: