Also it is on Multiplayer that I am seeing this issue. I tried it on creative in a superflat world and I could not duplicate it. I am not sure what is happening. I guess you can close this bug since I am not able to do it in creative, it must just be my server or something. Thanks for your time and sorry for the trouble.
I figured out it was not the latch that was causing it. It was the removal of the redstone torch that deleted the blocks. I also figured out its on most block types. I have tested on all types of stone blocks, I am not sure if this is an issue with anyone types. Also the block does not drop and turn into a floating entity, it just disappears. If I can narrow it down more, I will report back.
Yes our server does have a few. We are using Logblock,Lockette,Dynmap, craftirc,signcolours, wickMOTD. We are a craftbukkit server. I was not sure if this was a game code issue or something that came up with their code. We have been seeing blocks delete still and not redstone related now. A player was farming and the block that he either touched or placed our disappear. I have not opened a bug for craftbukkit but I can if you think this is related to their code since I was not able to reproduce on my single player map.