It seems they no longer function this way, but rather the way you had originally thought it should. I've done tests with this, and it only outputs a signal if the item is cleared. This is why I opened a separate issue; the enchant command outputs a signal if no item is enchanted. Why is inconsistant command block behavior not considered a bug? This issue has been resolved, and works just like the original poster thought it should. My issue has not been resolved, and thus should not have been flagged as a duplicate, unless there is some command block behavior I'm simply not understanding.
This bug has not been fixed. All of my redstone clocks keep freezing in 1.5.1. It doesn't happen as often. It used to happen every time a chunk was reloaded, but now it seems fairly random.
Sorry Gerrard for the late response. This has happened to me on single player maps and multiplayer maps, both of which were vanilla. It doesn't happen often, but I will attempt to upload a schematic the next time I encounter the issue.