I knew I would be shaving a ring of lead off each. Therefore I knew I would be stressing out the gun.
Tropico - I'm not sure how you came to the conclusion that you would be "stressing out the gun". If you mean that you would be damaging the gun let me assure you that's not the case - the gun was designed to be able to do that. Shaving the ring of lead is intentional and will not damage the gun. It seems much higher loads from the powder charge igniting. By the way, your url gives an error. You need to go to the home site first, then go the the cylinder loading stand using the drop down menus.
ncc1701a - It is true that a gap between the powder and the ball is not a good thing for the gun. It's also a good thing to compress the powder charge to get more consistent ignition and pressure, thus more consistent accuracies.
You didn't mention what type of gun you have (I don't know of any Uberti 44's with a 5 1/2" barrel), but I'm surprised that you don't get adequate compression with the gun's loading lever. Unless you are loading a large chamber gun like a Dragoon or Walker the gun's loading lever should be long enough to seat the ball on a 25 grain powder charge with no wad between.
You also don't mention what kind of bench loading stand you have. I'm aware of two, one of which is inadequate for many guns for just the reason you state. The one referenced by Tropico is the good one; I've used it with all my guns and it does an excellent job regardless of the cylinder geometry. It's also sold by Powder, Inc. for the same price, but they say they are out of stock and don't know when they'll be getting more.
As I understand your post you have verified, by using the two empty cases, that when loading the cylinder with the bench loading stand without using a felt wad that there appears to be a gap between the powder and the ball. You have not verified a gap exists when loading without a felt wad using the gun's loading lever. I can't assume that the problem you've seen with the bench loading stand is also present when using the gun's loading lever since the geometries could be very different depending on the stand you use. Therefore I can't say if you may have damaged your gun's cylinder. I rather doubt it, however, as any damage should be apparent by now.
My only suggestion is to use more powder or an inert filler when not using a wad.