hi,
A) HMD settings
the HMD (you use the Virtual Research V8 from what I know) needs 480 by 640 resolution and 60Hz.
B) GRAPHICS DRIVER
If this is the case, then I would suspect that output on one eye different than the other eye might have something to do with your graphics card / driver. please make sure you use the latest driver for your graphics hardware and (in case you use nVidia hardware) that you use horizontal span mode, NOT dualview.
See also
http://www.worldviz.com/support/hardware_faqs.html
for more details on this driver issue.
C) if nothing helps and one eye continues to look different from the other, run the HMD in mono mode (i.e. only provide input for the left eye) and see if one eye still shows funcky stuff. if yes, there is a problem with your HMD and you need to get in touch with Virtual research.
Please let us know if any of above helps.