Seamonkey 2.0.11 definitely does NOT work the same as Thunderbird 5.0. I played with it for a bit, and never could figure out how to get the filters to run on the existing message base.
Figured, "Hey, the search function will use the same RE as the filter, so I'll play around with searching." Out of the 500 messages I put there, it found THREE that met the criteria, but there were definitely more than that.
Best recommendation I can think of is to try Seamonkey 2.2 and see if the filtering has been updated the same as Thunderbird 5.0.