This issue happened to me as well as soon as I installed and ran Crafbukkit / Bukkit. I added myself to the ops, no issue anymore. I would imagine there is some sort of either protection that must be edited or something along those lines in order to eliminate it.
Here are some things I have found :
i made a server and my friend cant break blocks, i tried to make him op but it doesnt work.
but i can see him breaks the block and get the item and if he relog he can see he got the item.
i tried to redownload the bukkit server and still.
Win XP Sp3 x86
Server is vanilla (bukkit without plugins) (on the first time i had 1 plugin)
i dunno the build of craftbukkit but its the latest cuz i just redownloaded it as i said.
In response a user said :
Try to walk a couple of blocks away from spawn and try there.
A moderator said :
No, OPs can do it on the spawn.
Try a new world, maybe the current one is corrupted.
Major thing I see is that people keep saying things about it being a spawn protection from Craftbukkit and also to set up the permissions and check if the default group is set to build. [I have to do this as well.]
This is the plugin to do so if you currently do not have it : Permissions