I thought that it mainly only happens when big changes happen all at once on the codebase, like an svn update or applying a patch, but it appears to happen more randomly than that.
I have that flag set in the global settings(and it seems to stick there) and I have tried setting the project settings to use the global as well as setting it specifically for the project, either way it always reverts back to project-specific without the flag. The problem is, when I change the setting by adding the -std=c++11 flag, it gets saved to that file, and the eclipse indexer works, but seemingly randomly, at some later time, the indexer will start marking things as errors and when I check that file and the gui settings, they are both reverted back to the default state. When I check the language settings file, it accurately reflects what is set in the GUI.
The folder and file are both RW so that's not the issue. setting folder, is ignored in svn because I don't want it under version control.