FFMPEG - errors when combining videos - ffmpeg

Question

I have two .OGG files of similar size, FPS and duration. My goal is to combine them into a side-by-side presentation using FFMPEG. To this end I've tried the following cmd:
ffmpeg -i subject.ogg -vf "[in]pad=3*iw:3*ih[left];movie=clinician.ogg[right];[left] [right]overlay=100:0[out]" combined.ogg
Suffice to say that the resultant video is non-playable. During the combination process FFMPEG prints lots of errors that read like:
[Parsed_overlay_2 # 0x1eb7d3e0] Buffer queue overflow, dropping
What is this telling me?
Note:
both source files are playable
I padded the 'output' to be rather large in an attempt to understand the params
the placement of the 2nd video at 100:0 is arbitrary. Once I get the cmd working I'll move it to a better location in the output.
both videos began life as .FLV recorded from web cameras. I converted them to .ogg as FFMPEG didn't want to combine two .FLV files. If there is a better route to this, please let me know.
So - what's wrong with my parameters and what am I doing to cause these FFMPEG errors?
EDIT:
ffmpeg -i clinician.ogg
Input #0, ogg, from 'clinician.ogg':
Duration: 00:05:20.98, start: 0.001000, bitrate: 2273 kb/s
Stream #0:0: Video: theora, yuv420p, 500x500 [SAR 1:1 DAR 1:1], 1k tbr, 1k tbn, 1k tbc
Metadata:
SERVER : Red5 Server 1.0.0 RC1 $Rev: 4193 $
CANSEEKTOEND : true
ENCODER : Lavf54.31.100
Stream #0:1: Audio: vorbis, 8000 Hz, stereo, s16
Metadata:
SERVER : Red5 Server 1.0.0 RC1 $Rev: 4193 $
CANSEEKTOEND : true
ENCODER : Lavf54.31.100
ffmpeg -i subject.ogg
Input #0, ogg, from 'subject.ogg':
Duration: 00:05:17.60, start: 0.001000, bitrate: 1341 kb/s
Stream #0:0: Video: theora, yuv420p, 300x300 [SAR 1:1 DAR 1:1], 83.33 tbr, 1k tbn, 1k tbc
Metadata:
SERVER : Red5 Server 1.0.0 RC1 $Rev: 4193 $
CANSEEKTOEND : true
ENCODER : Lavf54.31.100
Stream #0:1: Audio: vorbis, 8000 Hz, stereo, s16
Metadata:
SERVER : Red5 Server 1.0.0 RC1 $Rev: 4193 $
CANSEEKTOEND : true
ENCODER : Lavf54.31.100

Answer 1

Converting to x264 was a great suggestion. That seemed to turn the tide.
Here are some notes for posterity:
to convert flv to x264 and correct audio sync issues:
ffmpeg -y -i subject_s_2242_r_1658.flv -async 1 -ac 2 -strict -2 -acodec vorbis \
-c:v libx264 -preset slow -crf 22 subject.mkv
to merge two x264 files into a single side-by-side file and put the two mono audio tracks into stereo in the resultant file:
ffmpeg -y -i clinician.mkv -vf: "movie=subject.mkv[right];pad=iw*2:ih:0:0[left];[left][right]overlay=500:0" \
-filter_complex "amovie=clinician.mkv[l];amovie=subject.mkv[r];[l][r] amerge" final.mkv
I was unable to install AVISYNTH (running on CentOS 6.2) but it does look like a great solution.

Answer 2

It is probably easiest to do this using Avisynth.
Make the following input.avs file:
a = AviSource("first.avi")
b = AviSource("second.avi")
StackHorizontal(a,b)
Then run ffmpeg -i input.avs output.avi ... plus any other options you want.
EDIT: Another way to do it (not fast) is to dump the frames from both files to png and combine them with ImageMagick (for example montage) or similar image processing tools.
#!/bin/bash
ffmpeg -i first.avi first_%05d.png
ffmpeg -i second.avi second_%05d.png
for file in first_*.png ; do montage ${file} ${file/first/second} ${file/first/output} ; done
ffmpeg -i output_%05d.png output.avi
This actually lets you do a lot more image processing than just side-by-side, you can do arbitrary scale/overlay/background/etc. The problem is that the N-th frame from one file may not be at exactly the same time as the N-th frame from the other file, if they are variable frame rate, this is something that AviSynth handles perfectly for you. If the clips are constant frame rate that is not a problem.
Combining clips by making a new clip containing both like this (whether through avisynth or not) requires recompressing the video, and reduces video quality/increases file size.
I am not sure how to read ogg files into Avisynth, but there is probably a way. Check the FAQ on input formats.
Side comment: The choice of theora/ogg is strange. Better: H.264 in mp4 container.