server side filters 1.4.x require suid binary program. If you installed program without suid bit set, it does not get privileges needed to modify your home directory.
server side filter 1.3x use ftp to access your home directory.
Where's this suid binary program you speak of? I didn't see anything about that in the ServerSideFilters plugin documentation nor am I able to find a binary in the serversidefilters plugin folder. :(
http://sourceforge.net/project/showfiles.php?group_id=95828
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