I've seen this too. I think it has to do with the way the 'loaded' units are displayed. In the past, they weren't greyed out or indented. Perhaps that was the only change made, and we're just starting to notice it because they're different now.
One of the things I learned in PTW to get around this (there was often confusion when unloading units) is to name the armies/transports. It won't change the way they're displayed, other than to say Elite* Calvary VIC in Army2 or somesuch. Renaming the transports/armies would also help in deciding which to attack with. Wouldn't do to attack with an army of infantry when you're trying to use the calvary.