Paul, Seq (short for Sequence) only exists in the context of Playlists.
So I'm guessing you've added the albums in question to a playlist. Once tracks are in a playlist, their original order on an album (the track #) is irrelevant: only the Seq matters.
Tracks are assigned a seq in the order in which they are added to the playlist, and the seq they get stays until you change it.
You can change the seq be resorting your list, and then clicking the Update Order button.
If you're talking about the Seq in "Playing Now", that is just a temporary Playlist. The Seq is assigned in the order items were added. The solution is the same: resort, and Update Order. The Update Order command is available by control-click (right click) on the zone, or from the dropdown menu on the Playing Now tab.
If you add a bunch of tracks to Playing Now (or any playlist) with one click, they are added in the order they are displayed in the view you added it from, so sort it the way you want before playing.
Make sense?