SU800 vrs SB900
Turn the onboard flash to "--" in the commander menu to remove it's contribution (except at very close range or High ISO where it's noticeable) or use FP Sync and shutter speeds over 1/320th if you need to eliminate it altogether.
Firing flashes in manual mode or using fv/lock will reduce the possibility of getting the aforementioned blinkers. TTL seems to be the worst culprit there.
I never tried an SU800 so can't comment.
Oh - you may find that using a piece of exposed film to gel the onboard will reduce it's contribution and still allow IR communication.. It's something I've read about but not tried myself.