Maybe the note on the bottom of page 108 holds the key:
Minimum shutter speed is ignored in favor of the option selected for Custom Setting e1 (Flash sync speed, 0234). Note that ISO sensitivity may be raised automatically when auto ISO sensitivity control is used in combination with slow sync flash modes (available with the built-in flash and the optional flash units listed on page 293), possibly preventing the camera from selecting slow shutter speeds.
What metering option was used? TTL-BL only works with matrix and center weighting not spot.
What was the color and brightness of the focus target? If the target was a large white object the exposure will be computed assuming that has an average 18% gray value.
As noted, it is best to set a fixed ISO for flash exposures. Remember that the camera is taking an ambient light exposure and a flash exposure. Auto is fine for ambient, but for the flash the Auto ISO will be different. I guess the camera is picking the ambient exposure value and the a speed less then the max flash sync speed.