When creating child thoughts off of pinned thoughts, the new child thought will link itself to (what I would call a random) thought in a completely un-related parent-child tree. This has been happening to me on a regular basis with 6.0. At first I thought maybe I was doing something wrong but it appears to work fine in 5.5.
See attached screenshot.
Windows 7 64-bit & Vista 64-bit
Java 6-update 20