Based on the knowledge base article about 3.0, I thought this was fixed, but the pending change set is still resetting the selection to the first item after a difference.
The selected file is still highlighted, but using the down arrow moves the selection to the top.
Okay, I just did this a minute ago, but now I can't reproduce it. There must be somthing else required to make this happen.
Pending Change Set Selection
Moderator: SourceGear