If you created a slider element and your images are not the same size – the issue are actually the images themselves. When using the slider image sizes, you need to make sure that your images have at least the sizes specified in the slider size options. For example, if your slider image settings are 1000x500px your images (used for the slider) should have at least 1000px in width and 500px in height. If the images are smaller the crop tool will just leave the images the same size that they we submitted and this creates problems with slider heights.
To fix this issue make sure you are using big enough images to present in the slider. If you are using custom slides – the images you upload should be big enough, if you are using the latest posts feature you need to be sure that the post featured images have at least the size you specified in the slider image crop settings.