iX Capture will have issues matching imagery if the naming is different or the event ID numbers do not match. There can be problems stitching over water as well, which can be solved by checking "generate large image despite error conditions". 16 Bit tiffs can only be created with the latest update.
In Depth
Camera type: Multihead must be selected in order to import 280 imagery. An equal number of L and R images must be present. The L and R images must have matching filenames and event ID. 
iX Capture cannot find enough tie points to combine L and R imagery when the image is mostly / all water. Checking "GENERATE LARGE IMAGE DESPITE ERROR CONDITIONS" will combine the images. A line may be noticeable between the two images, which is a result of the two images slight change in exposure or color.