CS3 Video Encoder not as good as FLIX?

I had the disturbing experience yesterday of having to ask my
client to encode their own flv for me to use. They had given me a
QT file, which for whatever reason, had a glitch in it that
prevented it from properly encoding on my stock CS3 video encoder
software. They don't have Flash, and are on a PC (I'm mac). They
encoded it using their Flix encoder, and talked about the newest
version ("S" or something like that). Case in
point, their flv worked and mine didn't. (Mine was playing fine,
but something in the metadata was getting goofed and not throwing
an end-of-file status flag for me to capture. So, I couldn't get
the program to automatically close the video and move on.) I
checked for an update to my CS3 encoder, which simply took me to
the basic "Adobe software update" software, which
suggested a few other updates that I'm assuming are irrelevant to
Flash. (Reader, Version Cue, Bridge, StartMeeting, After Effects).
So, my lengthy intro leads me to the question, "Is
my stock CS3 flv encoder not the best thing for encoding
(On2).?"
Is there an update or better solution I'm not aware of?
Thanks,
Greg
AntifreezeDesign.com

I've tested a few encoding options (Sorenson Squeeze, flix
on2, CS3 encoder)
Today we're using FlipFactory to encode our flv &
many more files but when I have a job to be done quickly I just use
the CS3 encoder, disregarding any other fancy features like 2pass
encoding I think that the CS3 encoder is pretty good and it writes
ALL the needed metadata.

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