There is a folder "test" in both, c:\ and d:\. On d:\ it's empty, on c:\ it contains:
dir /b /w /s wrote:C:\test\usr
Src is "c:\test", Dst is "d:\test", Filter string is "usr\home\foo*" (see Screenshot below, sorry for German translation, hope it's okay nevertheless).
Result is "No files were found to synchronize!"
When just switching to "Exclude folders" (with the same Filter string), home.pwd and bar.pwd are compared (see screenshots below).
Using e.g. "*foo*" as Filter string leeds to exactly the same Results. However, "\usr\home\foo*" as Filter string compares nothing when used for filtering and compares all three files when used for excluding.
When I start to take Path-Components from Filter string into Src and Dst, with Src "c:\test\usr", Dst "d:\test\usr" and Filter string "home\foo*" Results are like above. With Src "c:\test\usr\home", Dst "d:\test\usr\home" and Filter string "foo*" for excluding Result is like above and for filtering foo.pwd and home.pwd are compared (home.pwd as mentioned above without being matched by Filter string).
I hope, this environment could be easy reproduced. But maybe results don't happen on every system (actually tested on WinXP Home 2002, SP3).