Neptune doesn't do any processing of the video - that's entirely up to the jAlbum core. jAlbum is probably misreporting the dimensions of the processed video.
Please give me a link to the original video. It's probably too large to attach to a post here, so just upload it somewhere that I can get to.
BTW, there's usually one quick tip-off that the orientation flags in a video are wrong. When you add the video to the album project, look at the thumbnail that jAlbum creates in the main Explore window. Is it correct? If it's improperly rotated, you need to rotate it in jAlbum before making the album. Select the thumbnail and use the rotate icons to get the thumbnail in the correct orientation before making the album. See screenshot.
Once in a while you might encounter a video that is more of a challenge, one that strenuously resists the proper orientation. Post back if you run into one of those - there are other tools that can be employed.