I'm using 2009.1.526.
I can repro the same issue in your attached application (clearfilter526.zip
1) Click Filter on Subject by checking (Cats are cool)
2) See that it's filtered to show only "Cats are cool"
3) Click button (Clear Filter)
4) Now Filter on Subject by checking (Mice are cool). (Uncheck all others)
Filter works on Mice are cool
Filter no longer works after clicking (Clear Filter)