You were actually pretty clear the first time around. And what you describe sounds impossible.
My best guess is that you are accidently not looking at the same logfile you are writing to. Or that you are looking at "old" stuff in the logfile while current content is still buffered and not written to the file yet.
Console 1:
Code:
rw@jodel:~$ cat > fifo
Hello
this line shouldn't show
Jelly
rw@jodel:~$
Console 2:
Code:
rw@jodel:~$ cat fifo | grep ll | tee log
Hello
Jelly
rw@jodel:~$ cat log
Hello
Jelly
rw@jodel:~$