I've noticed that when alternating between fingers or alternating between up and down strums with a pick that it can really change the tone of a bassline. When I really got this was when I was trying to play a bassline to a certain song. I was playing the right notes, but it just sounded off. Then I played it over again but starting on the opposite finger; bingo. The same applies to picking. Some riffs start with an up-strum. Some with a down-strum. You have to listen for which one to use. I know a lot of you are aware of this, but I didn't know it at first. I had to use my ears. If you haven't tried it, try leading with a different finger when you alternate, or if you always pick starting with a down-strum, try starting with an up-strum.