Sorry for the triple post, but the content really doesn't seem to belong in the same post.
For reference the application I am working on is 3d game and game library. It is split up into 3 Code::Blocks projects. "Physgame" is the library, "EngineDemo" is a unit test and place try all the features of Physgame, and "Catch!" is the actual game. Right now I am working in the EngineDemo to test some new functionality we just added to Physgame. EngineDemo and Catch! both link to Physgame and not much else, and Physgame links to several external libraries and provides a single interface to the required functionality of Ogre3d, bullet3d, ticpp/tinyxml, Boost, SDL and certain OS dependent functionality.
Currently Physgame is single threaded, but Ogre3d and Bullet both spawn separate threads to perform some of all of the work they do. These are both well tested, and the issue I am having has existed before and after having changed library version. For example When we moved from Ogre 1.7.0 to 1.7.1 the issue still existed, it would simply pause somewhere else.
I would also like to note that sometimes, the issues simply does not occur. After certain major code changes the run and debug buttons would work, other times only one or the other would work. Right now neither work. When using the Debugger is pauses when I am initializing the Logger, sometimes after Ogre has finished it's initialization and sometimes not. When using the run button currently it is pausing just after the window and 3d rendering canvas are displayed, but before anything is rendered.
Edit: While writing this it occurred to me that this could be some kind of Race condition that the extra overhead of having and IDE could cause. I thought maybe physgame is trying to call on Ogre or Bullet Components before that have finished initialising. I tested this by putting a 1.5 second delay in between initializing Ogre and when it is first called, and it still crashes in the exact same place when both debugging and running it. I will try playing with LD_LIBRARY_PATH next.