Dispensers are not properly dispensing every time; only some of the time. I discovered this as follows:
I tried to use my fully automatic TNT cannon that works in 1.5 in 1.5.1 and it doesn't work. I have it completely exposed to see all the circuitry, and the dispensers are indeed receiving the correct signal - they are even clicking upon receiving it - but no TNT is coming out (despite my triple, quadruple, and quintuple checks that there is, in fact, TNT in the dispensers). The only thing that seems to get them to dispense TNT is to trigger a block update (neither redstone current nor rearranging the contents of the dispenser will trigger such an update) for the dispenser, and this only works some of the time and then only for a very short period of time (30 seconds to a minute) before the dispenser ceases to work again. Sometimes, one section or another will go once, but not the next time, or the time after that, and then a minute or two later the other section will go once, then the first again, then both, etc, etc, pseudo-randomly ad infinitum.
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I have uploaded a schematic of the cannon, as well as screenshots. The schematic isn't perfect, since MCEdit doesn't recognize all the 1.5 blocks properly yet.
In case you were wondering: no, I did not use any mods/utilities to build this cannon or do anything to my world save, etc, etc - this is entirely a manual project done in vanilla Minecraft.
Duplicate of MC-12464?
Not necessarily a duplicate, because I'm powering my dispensers from below, and he specifically states that the problem only affects blocks on top of the dispenser, not blocks beneath it; however, I am seeing symptoms which closely match his.
My guess is that the same code is responsible in some way, perhaps behaving itself differently in 1.5.1 (when I had my problem) than in 1.5 (when he claims to have had his).
I'm having this problem as well... Got some downwards-facing dispensers with water buckets in them. Pressing a button sends them one signal, and another signal after a long delay (70 ticks or so). The signals will be completely ignored if the dispenser(s) haven't gotten an update. All my dispensers are being powered by a wire ontop of them. If two dispensers are next to each other though, they will update each other every time, and there shouldn't be a problem. Because of this I tried to put droppers next to each of the dispensers that weren't working, hoping that the droppers would update the dispensers, but this only solved half of the dispensers.
Hope this helps a bit for debugging and solving the problem.
@[Mod] Tails
Is that using the cannon specs I uploaded? It can be somewhat misleading since the cannon appears to fire, but not all three rows of dispensers are going off (I believe the side dispensers go off, or the bottom only, not both; I can't remember which way it goes, since I deserted the project for others some time ago as a result of this bug, to be resumed when it was fixed). No offense - just wondering. If it really is fixed, great!
Please provide screenshots of your setup.