Horrible horrible stuff that made logic gates illogical, made my brain hurt...
I managed to narrow it down to it being the redstone torch and the block it's on/in that is bugged. I've managed to create a pulsar in SMP using nothing but repeaters and a button to start it, and it works perfectly. A normal pulsar including torches = a dead pulsar.
Also it's not just pulsars. Logic gates aren't properly working due to these bugs. Moving the gate itself a few blocks over seems to fix this problem for a short while, only to have the problem come up again, maybe once the chunk unloads, I dunno.
My point is that redstone torches aren't functioning correctly in SMP, and for a person who loves redstone as much as I do, this is a very painful bug. I haven't managed to find it in the upcoming bug fixes, but it would be greatly appreciated.