alexks3, you need to be using Adium 1.0b1 or higher. Then just go into Preferences, Messages, select ProtoScroll (or another style that supports transparency, check the Use custom background box, and then click on the Color box. Lastly, drag the Opacity slider to a desired value (say, 60%), and you're done.

No, I'm afraid Proteus does not have a fix. You see, the actual scrolling is the responsibility of the messageview, not the client. There isn't really anything Proteus itself can do. As for smooth-scrolling messageviews in Proteus, their only "fix" has been to remove the smooth scrolling feature. I'm not really willing to update ProtoScroll until I figure out a way to keep smooth scrolling, because that's the whole point of this messageview.

Thanks for the comments, everyone. Regarding mathuaerkneam's inquiry about scrolling at the very beginnings of conversations: this is possible, but it is not practical, because I would need to "force" the scrolling. The main problem with doing this is that if you have scrolled up to look at some earlier part of the conversation, if the other party sends you a message, it will scroll back down whether you like it or not. If this is confusing, try it with some themes in Proteus that use a very similar script; you're reading an earlier message, and all of a sudden you're interrupted. It's really annoying.

I believe I could fix this by adding some whitespace at the beginning, so the Javascript "thinks" there's already a conversation going. If anyone has ideas just email me or something.

To do:
It looks like there's a minor display bug with long away messages; I'll fix that in the next release. Also, it looks like people want some choice as to what font to use for the name of the person you're talking to, so I'll have a few choices for that in the next release also.

Again, thanks for the comments!