At some point apr and apr-util (for me version 1.2.2) were changed from slot 0 to slot 1. Unfortunately, a slot move such as: slotmove dev-libs/apr 0 1 was not added to the profile updates, so the changes were never applied to the slot information in /var/db/pkg. That said, when checking for collisions, the /var/db/pkg apr reported slot 0, and the new apr (1.2.7-r3) reported slot 1. Having different slots, this caused collision-protect to fail.
I didn't even realize there was such a beast, now I do. However I can't find any documentation on it, is this correct? If so I'll add it to updates/Q3-2006 slotmove =dev-libs/apr-1* 0 1 slotmove =dev-libs/apr-util-1* 0 1 Also, there is still a collision between the slots that we still need to address, I'm hoping I'll have time to fix that this weekend. See bug 114953.
slotmove is now in CVS.