I don't think this was ever documented with a bug report, but there have been major issues with moving clips in takes, especially (IME) when some take lanes had already been deleted.  Clips would disappear, or end up dropped somewhere other than intended.  Others have noted similar buggy behavior.  It was better in X3d, but still buggy.  This was one of my personal major issues with take lanes so I was eager to see if it was fixed. I am happy to say it seems to be fixed in X3e! 
 
So far I am very pleased with X3e.  Thanks CW.