Nice, how did you make the timed pulser? Did you use the daylight sensor? Does the pulse then activate the redstone circuit which might've gotten stuck or what?
I tried something similar in the mob factory by using minecart on a pretty sloped track, which also works when the server reloads. The problem is just that the pistons now glitch instead.
Also what do you think of this logo? UBSR Redstone?
The clock is the same setup as yqt's, just with a much shorter time. What I did was take the daylight sensor output (coming from the right side of the screenshot) to act as a type of gate using the comparator (NOT gate? no idea) which stops the pulses from going through during the day and at night allows it to go through. At night, the pulses go through and the repeaters beyond the comparator are for fine tuning the timing.
The repeater before the comparator is needed because the ultra-short pulses make the comparator act oddly. Although you could turn that odd behavior into something like a transistor, which is what it seems to act like without the repeater.
I put the repeater on the output from the daylight sensor to smooth out the flickering when it transitions from day to night or night to day. Might not actually be needed.
Nice redstone logo I guess. I don't want that in a texture pack though.