I ladle cast. I tried using the bottom pour, but wasn't satisfied with the process. First of all, I had large weight differences with bottom pour, much like you are describing. I also has much poorer "fillout" with bottom pour, my bullets didn't seem to always fill out completely, there always seemed to be something not quite right, often an incompletely filled out band at a lube groove. So I tried the ladle. I had nothing to lose, I had already made up my mind to quit casting if I couldn't produce uniform, quality bullets.
So I bought a ladle, and converted it to left-hand use, and went to it. The first thing I noticed was my bullets were slightly heavier. They were uniform & well filled out (this is the short version, it required some experimentation to get to this point). With the bottom pour I had little black specs in some of my bullets, and these bullets were always lighter than the miserable few "good" bullets I produced. I would melt these bullets down to find out what the contaminant was, but there was never anything there but lead.
I finally came to the conclusion that I was aerating the alloy when I used the bottom pour. The specs I saw were tiny air bubbles. I had tried both a LEE bottom pour, and a Lyman, with the same results. When I ladle cast, I only fill one cavity at a time, and pour the excess lead from the ladle over the hole in the sprue plate, like I was still trying to fill the cavity. I think this keeps the bullet somewhat molten, and allow air to escape over a longer period of time. I feel this is what gives me heavier bullets, with much greater weight consistency, and such greater quality.