Check the layers list and make sure that the bottom most layer is the layer that is your desired repeat size. To discern the size of the layer, select it and look for the W and H at the top left corner of the RS window. When the repeat is started it will use the bottom most layer as the repeat size. To re-order the background layer, hit Stop to stop the repeat and then click and drag the layers in the layer list so that the layer with the repeat size is at the bottom of the list. To change the size of a layer, you can use the crop tool, or go to edit > canvas size to adjust the parameters of that layer or edit>scale image to scale that layer.
For more information please email support@aquariodesign.com for further assistance.