I and a variety of people at my company are having a similar problem. If I'm doing a repeat command, for example to add several piping clamps on to a channel, some of the clamps go to the end of the model tree, but others go into random places up the model tree. This produces problems where components high up in the tree are dependent on components at the end. A lot of times those components also can't be reordered.
The easy fix is not to use the Repeat command of course, but that command is handy in some cases.
Anyone else having this problem?