/filter -cffx infile outfile $crlf is indeed buggy (it does nothing), but your problem is not related to this bug. You're dealing with custom windows, where there can be no empty lines. The blank lines you see in custom windows when you /loadbuf a file with empty lines aren't actually empty; they consist of a single space. You can quickly verify this with
//echo -s $replace($line(%t.w_s,3),$chr(32),@)
You should see a "@" echoed in Status.
So, to filter out these lines from your window, you'd have to use a pattern that matches lines consisting of one space character. You can do this easily with the -g (regex) switch:
filter -cwwxg %t.w_s %t.w_s ^ $