I, too, am having this issue. I actually have two problems with this warning. First - when I import several parts and I need to organize them, every time I move something, it pops the warning up. It's frustrating because I know that it's out of range, that's why I'm rearranging it. I don't need that warning every time I move something. I need that warning when I click print and something is out of range.
Second, and strangely, I'm currently getting that same warning with two pieces that are well within bounds and the warning goes away when I select a raft. But then complains when I get rid of the raft. This seems like a legitimate bug to me, as I can't think of how having a smaller footprint would put me out of bounds.