We've been experiencing unpredicatble behaviour with our blocks as well. By default, we have the following blocks displayed in a course view:
People HTML Block
Activities Latest News
Search Forums Upcoming Events
Administration Recent Activity
With editing turned on, moving blocks between columns, and up or down within a column, means that some blocks disappear. For instance, if I move "Recent Activity" to the left column, "Search Forums" will disappear. As soon as it disappears, it is included in the drop-down list of blocks that can be added.
So I add it back again. It appears in the right-hand column. If I then try to move "Recent Activity" up one position in the left-hand column, it disappears, only to be replaced by "Search Forums". This means there are two instances of "Search Forums" and no instances of "Recent Activity".
I've tagged this as Major because it's worrying our users a lot.
You can recreate this problem on our test server:
Log in as "moodletracker" with password "moodletracker"