I'm having the same problem that is documented at http://groups.google.com/group/jquery-en/browse_thread/thread/976e49897120d95c?tvc=2, but can't reply to that thread (too old?).
To summarize the problem, with IE6, when blockUI is called the select boxes dissappear. When unblockUI is called they reappear. I have a form that has a number of multi-line select boxes, therefore this problem is very noticeable. The referenced thread above hinted at a fix, but didn't provide any details. Any ideas would be appreciated.