I have had the same experience once in a while, especially when making some small tweaks on something which require almost constant shutdownofp-maketweaks-overwriteoldpbo-restartofp..
I've always thought of it as some sort of windows+memory problem rather than an ofp problem..
I also have sometimes seen ofp read the wrong config from an addon, for example if you rename the existing config.cpp to configold.cpp and add a new config.cpp to test some changes ofp can still read the old config, the configold.cpp too..
Experienced this with some userActions stuff where the old actions (in the configold.cpp) and the test stuff were both available although the test config.cpp did not include any the old stuff...
This may be related to the above 'problem' though...
I could go on pages and pages on what weirdness OFP can throw at you sometimes...