After a month of talking over the phone with Microsoft tech support and more than a month and a half of struggling with then problem and trying to isolate the cause; I put together a short article on how to lose your data with merge replication if you use parameterized row filtering and upgrade your publisher from SQL Server 2000 to SQL Server 2005.
The details of the problem, steps to reproduce the behavior and scripts can be found on this article published on DevX:
SQL Server 2005 Bug Alert: Merge Replication Could Mean Data Loss
My main purpose is to speed up the resolution, so any comments, workarounds or similar cases you might find, please give me a shout.
Have a great weekend!