I was able to solve this problem by adjusting the default.css file for the message pane in my system.

I couldn't reproduce this problem. So you have more messages in the room than the message-pane is high and at least parts of the message is hidden?
Does it depend on the size of the message or something like that?

Yes, so the number of chat messages has filled up the pane and the most recent message gets hidden at the bottom under the input field. Once another message comes in it bumps it up the hidden message. So if you are chatting with someone you may find yourself one message behind the conversation which is a strange sensation.

The length of the chat message doesn't seem to matter. It's more about total number of chat messages that fill the space available.

default.css:
.message-pane-wrapper {
bottom:62px
}

seems to solve the issue. Tested with Chrome 40.0.2214.93, FF 36.0, IE8 and IBM Notes 9

@melissanoelle / @bklang: Is this of interest?

@nesges Thank you, that worked. I've created a PR based on your fix.