One user writes: "Copied a selection, pasted it, merged down, double-clicked a couple of times with the selection tool and *crash*." I can reproduce this. Crashes as such:

Thread 0 Crashed:
0 libobjc.A.dylib 0x908311f4 objc_msgSend + 0x14
1 com.apple.CoreFoundation 0x901913e8 CFEqual + 0x120
2 com.apple.CoreFoundation 0x901b51b0 CFArrayGetFirstIndexOfValue + 0x218
3 com.apple.Foundation 0x90a1fc7c -[NSCFArray indexOfObject:] + 0x64
4 org.opensword.pixen 0x0001a85c -[PXCanvas setLayers:] + 0x34 (PXCanvas.m:197)
5 org.opensword.pixen 0x00030c30 -[PXRectangularSelectionTool setLayers:fromLayers:ofCanvas:] + 0x70 (PXRectangularSelectionTool.m:106)
6 org.opensword.pixen 0x000308b8 -[PXRectangularSelectionTool mouseDownAt:fromCanvasController:] + 0x110 (PXRectangularSelectionTool.m:69)

This just happened because Merge Down wasn't designed to be used with selection layers. Fixed to act the same way as "deselect" when you're trying to Merge Down a selection.