I have the same issue.
Version: 3.0.4
OS: Linux CentOS
Java: Oracle 1.7.0_04-b20 (7)
Bukkit Plugins: LogBlock, Light Weight Chest Protection, WorldGuard, WorldEdit, PermissionsEx, ModifyWorld, CommandBook, ChatManager, DynMap.
Description of Problem: Turtles are unable to destroy blocks, however blocks can be placed.
Error Messages / Link to pastebin of log: When the turtle API is used to dig there are no error messages in the console, or indeed any messages of any kind. I have turned on debug mode for permissionsex and that also shows nothing.