Sounds like you mean that a couple of messages have gone missing, rather than threads. A "thread" is an entire conversation, a root message plus one or more reply messages. If you can identify which thread those messages were a part of, I can go look for the messages. The thread's root subject line would do it, or the ID # that's part of the URL.

If you prefer the black-on-white color scheme for the table of contents, the Nexus has that. Click Settings..., and select "black-on-white" from the list under "Table of contents theme". Then click the Remember button to set a cookie so that it shows up in the future.