A multi-gallery album generated by jAlbum and the Juicebox Skin displays and functions fine on my iPod Touch iOS 5.1.1.
If you do not like the Splash Page and would like the gallery to initially appear, you can set showSplashPage="NEVER" in the Pro Options text area.
If you like, you could also set screenMode="LARGE" to force the gallery to be displayed as if it were on a device with a larger screen.
If you do not like the way the web page is scaled on a mobile device, you could add the following line of code to the <head> section of your album's 'index.html' page:
<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1">
If you would rather simply create a single gallery like JuiceboxBuilder or the Lightroom, Photoshop or Picasa plugins (rather than a multi-gallery album with a navigation tree menu), then go to 'Album -> Settings -> Advanced' and deselect the 'Process subdirectories' checkbox. jAlbum will then process only those images in the root input folder and a single gallery will be created which will look identical on an iPhone (or any other device) to a gallery created by any other method.