The default setting of JRiver rips to Artist, Album, and then Track. If you have a multiple artist CD, the tracks can be split up among several folders. You are probably expecting them to all be in one folder. JRiver's views aren't dependent on how the files are stored so you can still see the entire album. If you want the CD's kept together, you can change the File Location options under Tools > Options > File Location > Audio > Folder Rule.
For the files you have already ripped you can use Library Tools to move them to folders based on Album.