Regardless of the permissioning issue moving forward, I did a locate on ffmpeg and took a whack at where it is installed, and added the following to my _config.php:
FLV::set_ffmpeg_root("/usr/ports/multimedia/ffmpeg");
Then I ran the command again:
ffmpeg -y -i /usr/home/gfisher/assets/Uploads/section1.flv -an -s 640x480 -ss 1 -an -r 1 -vframes 1 -y -vcodec mjpeg -f mjpeg
And this is what I got:
$ ffmpeg -y -i /usr/home/gfisher/assets/Uploads/section1.flv -an -s 640x480 -ss 1 -an -r 1 -vframes 1 -y -vcodec mjpeg -f mjpeg
ffmpeg version 0.4.9-pre1, build 4718, Copyright (c) 2000-2004 Fabrice Bellard
built on Oct 20 2009 12:23:28, gcc: 3.4.4 [FreeBSD] 20050518
[flv @ 0x280d2008]skipping flv packet: type 18, size 224, flags 0
[flv @ 0x280d2008]skipping flv packet: type 18, size 4121, flags 0
Input #0, flv, from '/usr/home/gfisher/assets/Uploads/section1.flv':
Duration: N/A, bitrate: N/A
Stream #0.0: Audio: mp3, 44100 Hz, stereo
Stream #0.1: Video:
ffmpeg: unrecognized option '-vframes'
Are we getting anywhere??