This has been an issue for me for quite some time (since WordPress 3.0 release I believe), but it has yet to be resolved.
I have multiple fields with the htmlEditor enabled. All the buttons seem to work just fine (bold, lists, etc.) except for the Link. Selecting text and clicking the link button used to bring up the URL box, but now it seems to just jump the cursor up into the main post window. I have no need for the full TinyMCE editor in these fields, but occasionally do need a link in there, and typing them in manually is getting tedious.
Please advise. I love this plugin and I'd love to see a fix for this issue!