In the most recent versions of Minecraft (14w31a, possible as old as 14w29a) fill clocks and setblock clocks run slower than in previous versions (If you don't know what these clocks are, see SethBling's redstone videos). Fill clocks, the fastest clocks in MC, used to run 20 times per second, as that was how many game ticks there were per second. Now, it seems to run about 8-10 times per second, I can't determine it exactly. Setblock clocks are also affected, running visibly slower and producing less noise. This is problematic as it interferes with scoreboard timers.