Using WP 3.0 and RB Internal Links 2.0.12, I have noticed a couple of issues.
When filling in a custom link txt just before I insert the link, the custom link txt is sometimes shown after the link: http://easycaptures.com/3563544336, in stead of replacing the post title. The post looks like this in editor: http://easycaptures.com/7039932152
Earlier today I had a perhaps related issue. In a paragraph I had two links without custom link text. RB Internal Links did not include the post title and all the text from the beginning of the first link to the end of the second was underlined (because of the a tag).
I wonder whether there is something unstable going on with the replace function?