I checked out latest and had to do a small bit of changes to sync the 
timestamps of the two cameras whenever frames have very close 
timestamps.  So they aren't EXACTLY synced, but VERY closely synced.  I 
can try to send you a screen shot of the output.  Note, I am testing 
this with a quite small checkerboard (your checkerboard, but with 26mm 
squares).  Maybe that's the problem?  Maybe I'm sampling a space too 
close to the cameras?

Eric Perko wrote:
> Patrick,
> 
> What version of camera_calibration are you using? Boxturtle?
> 
> - Eric
> 
> On Tue, Apr 6, 2010 at 4:31 PM, Patrick Beeson <beeson.p@gmail.com> wrote:
>> I'm trying to calibrate two identical 1394 cameras that are sitting next
>> to each other.  The stereo calibration from camera_calibration converges
>> to VERY bad R and T matrices, rotating the frames and
>> the warping the images drastically.  I've tried several times, with no luck.
>>
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