Please consider contacting AJA Technical Support via phone or email for assistance. You may reach them between 9am and 5pm PST.
In all likelihood, the issue is related to the fact that the material is a sub-frame rate and not an "over-the-wire" frame rate. 720p 23.98, 720p 24, 720p 25 and 720p 29.97 are sub-frame rates within the larger over-the-wire frame rates of 720p 50, 720p 59.94 and 720p 60. If you have configured the AJA Control Panel application for 720p 23.98, you will not produce a video output that the monitor will understand; in fact, the AJA Control Panel Format tab will indicate "Intermediate only - secondary output format must be selected" if only 720p 23.98 is selected. For 720p 23.98, you may cross convert to 1080PsF 23.98 for video monitoring. Since you don't state which type of monitor you are using, be sure that it supports 1080PsF 23.98 if you perform a cross conversion; HDMI monitors do not support 1080PsF 23.98 for example. You should also keep in mind that any AJA Control Panel format selections and configurations should be made prior to launching Final Cut Pro X. You can find information and guidelines for using the AJA beta driver with Final Cut Pro X v10.0.3 in the FCP_X_and_AJA.pdf document that was included in the download alongside your driver installer and the operation manual for the KONA product.
Again, please feel free to contact AJA Technical Support for assistance.
AJA Video Systems
+1 (530) 274-2048 Intl.
(800) 251-4224 US